#!/usr/bin/env python
#coding: utf8
"""
General purpose utilities functions for fabio
"""
# get ready for python3
from __future__ import with_statement, print_function
import re, os, logging, threading, sys
import StringIO as stringIO
logger = logging.getLogger("fabioutils")
from .compression import bz2, gzip
import traceback
from math import ceil
FILETYPES = {
# extension NNNimage fabioclass
# type consistency - always use a list if one case is
'edf' : ['edf'],
'cor' : ['edf'],
'pnm' : ['pnm'],
'pgm' : ['pnm'],
'pbm' : ['pnm'],
'tif' : ['tif'],
'tiff' : ['tif'],
'img' : ['adsc', 'OXD', 'HiPiC', 'raxis'],
'mccd' : ['marccd'],
'mar2300': ['mar345'],
'sfrm' : ['bruker100'],
'msk' : ['fit2dmask'],
'spr' : ['fit2dspreadsheet'],
'dm3' : ['dm3'],
'kcd' : ['kcd'],
'cbf' : ['cbf'],
'xml' : ["xsd"],
'xsd' : ["xsd"],
}
# Add bzipped and gzipped
for key in FILETYPES.keys():
FILETYPES[key + ".bz2"] = FILETYPES[key]
FILETYPES[key + ".gz"] = FILETYPES[key]
# Compressors
COMPRESSORS = {}
dictAscii = {None:[chr(i) for i in range(32, 127)],
}
try:
lines = os.popen("gzip -h 2>&1").read()
# Looking for "usage"
if "sage" in lines:
COMPRESSORS['.gz'] = 'gzip -dc '
else:
COMPRESSORS['.gz'] = None
except Exception:
COMPRESSORS['.gz'] = None
try:
lines = os.popen("bzip2 -h 2>&1").read()
# Looking for "usage"
if "sage" in lines:
COMPRESSORS['.bz2'] = 'bzip2 -dc '
else:
COMPRESSORS['.bz2'] = None
except Exception:
COMPRESSORS['.bz2'] = None
[docs]def deprecated(func):
"""
used to deprecate a function/method: prints a lot of warning messages to enforce the modifaction of the code
"""
def wrapper(*arg, **kw):
"""
decorator that deprecates the use of a function
"""
logger.warning("%s is Deprecated !!! %s" % (func.func_name, os.linesep.join([""] + traceback.format_stack()[:-1])))
return func(*arg, **kw)
return wrapper
[docs]def pad(mystr, pattern=" ", size=80):
"""
Performs the padding of the string to the right size with the right pattern
"""
size = int(size)
padded_size = int(ceil(float(len(mystr)) / size) * size)
if len(pattern) == 1:
return mystr.ljust(padded_size, pattern)
else:
return (mystr + pattern * int(ceil(float(padded_size - len(mystr)) / len(pattern))))[:padded_size]
[docs]def getnum(name):
"""
# try to figure out a file number
# guess it starts at the back
"""
stem , num, post_num = numstem(name)
try:
return int(num)
except ValueError:
return None
[docs]class FilenameObject(object):
"""
The 'meaning' of a filename ...
"""
def __init__(self, stem=None,
num=None,
directory=None,
format=None,
extension=None,
postnum=None,
digits=4,
filename=None):
"""
This class can either be instanciated by a set of parameters like directory, prefix, num, extension, ...
@param stem: the stem is a kind of prefix (str)
@param num: image number in the serie (int)
@param directory: name of the directory (str)
@param format: ??
@param extension:
@param postnum:
@param digits: Number of digits used to print num
Alternative constructor:
@param filename: fullpath of an image file to be deconstructed into directory, prefix, num, extension, ...
"""
self.stem = stem
self.num = num
self.format = format
self.extension = extension
self.digits = digits
self.postnum = postnum
self.directory = directory
self.compressed = None
if filename is not None:
self.deconstruct_filename(filename)
[docs] def str(self):
""" Return a string representation """
fmt = "stem %s, num %s format %s extension %s " + \
"postnum = %s digits %s dir %s"
return fmt % tuple([str(x) for x in [
self.stem ,
self.num ,
self.format ,
self.extension ,
self.postnum ,
self.digits ,
self.directory ] ])
__repr__ = str
[docs] def tostring(self):
"""
convert yourself to a string
"""
name = self.stem
if self.digits is not None and self.num is not None:
fmt = "%0" + str(self.digits) + "d"
name += fmt % self.num
if self.postnum is not None:
name += self.postnum
if self.extension is not None:
name += self.extension
if self.directory is not None:
name = os.path.join(self.directory, name)
return name
[docs] def deconstruct_filename(self, filename):
"""
Break up a filename to get image type and number
"""
direc, name = os.path.split(filename)
direc = direc or None
parts = name.split(".")
compressed = False
stem = parts[0]
extn = ""
postnum = ""
ndigit = 4
num = None
typ = None
if parts[-1] in ["gz", "bz2"]:
extn = "." + parts[-1]
parts = parts[:-1]
compressed = True
if parts[-1] in FILETYPES.keys():
typ = FILETYPES[parts[-1]]
extn = "." + parts[-1] + extn
try:
stem, numstring, postnum = numstem(".".join(parts[:-1]))
num = int(numstring)
ndigit = len(numstring)
except Exception, err:
# There is no number - hence make num be None, not 0
logger.debug("l176: %s" % err)
num = None
stem = "".join(parts[:-1])
else:
# Probably two type left
if len(parts) == 1:
# Probably GE format stem_numb
parts2 = parts[0].split("_")
if parts2[-1].isdigit():
num = int(parts2[-1])
ndigit = len(parts2[-1])
typ = ['GE']
stem = "_".join(parts2[:-1]) + "_"
else:
try:
num = int(parts[-1])
ndigit = len(parts[-1])
typ = ['bruker']
stem = ".".join(parts[:-1]) + "."
except Exception, err:
logger.debug("l196: %s" % err)
typ = None
extn = "." + parts[-1] + extn
numstring = ""
try:
stem , numstring, postnum = numstem(".".join(parts[:-1]))
except Exception, err:
logger.debug("l202: %s" % err)
raise
if numstring.isdigit():
num = int(numstring)
ndigit = len(numstring)
# raise Exception("Cannot decode "+filename)
self.stem = stem
self.num = num
self.directory = direc
self.format = typ
self.extension = extn
self.postnum = postnum
self.digits = ndigit
self.compressed = compressed
[docs]def numstem(name):
""" cant see how to do without reversing strings
Match 1 or more digits going backwards from the end of the string
"""
reg = re.compile(r"^(.*?)(-?[0-9]{0,9})(\D*)$")
#reg = re.compile("""(\D*)(\d\d*)(\w*)""")
try:
res = reg.match(name).groups()
#res = reg.match(name[::-1]).groups()
#return [ r[::-1] for r in res[::-1]]
if len(res[0]) == len(res[1]) == 0: # Hack for file without number
return [res[2], '', '']
return [ r for r in res]
except AttributeError: # no digits found
return [name, "", ""]
#@deprecated
[docs]def deconstruct_filename(filename):
"""
Function for backward compatibility.
Deprecated
"""
return FilenameObject(filename=filename)
[docs]def construct_filename(filename, frame=None):
"Try to construct the filename for a given frame"
fobj = FilenameObject(filename=filename)
if frame is not None:
fobj.num = frame
return fobj.tostring()
[docs]def next_filename(name, padding=True):
""" increment number """
fobj = FilenameObject(filename=name)
fobj.num += 1
if not padding:
fobj.digits = 0
return fobj.tostring()
[docs]def previous_filename(name, padding=True):
""" decrement number """
fobj = FilenameObject(filename=name)
fobj.num -= 1
if not padding:
fobj.digits = 0
return fobj.tostring()
[docs]def jump_filename(name, num, padding=True):
""" jump to number """
fobj = FilenameObject(filename=name)
fobj.num = num
if not padding:
fobj.digits = 0
return fobj.tostring()
[docs]def isAscii(name, listExcluded=None):
"""
@param name: string to check
@param listExcluded: list of char or string excluded.
@return: True of False whether name is pure ascii or not
"""
isascii = None
try:
name.decode("ascii")
except UnicodeDecodeError:
isascii = False
else:
if listExcluded:
isascii = not(any(bad in name for bad in listExcluded))
else:
isascii = True
return isascii
[docs]def toAscii(name, excluded=None):
"""
@param name: string to check
@param excluded: tuple of char or string excluded (not list: they are mutable).
@return: the name with all non valid char removed
"""
if excluded not in dictAscii:
ascii = dictAscii[None][:]
for i in excluded:
if i in ascii:
ascii.remove(i)
else:
logger.error("toAscii: % not in ascii table" % i)
dictAscii[excluded] = ascii
else:
ascii = dictAscii[excluded]
out = [i for i in str(name) if i in ascii]
return "".join(out)
[docs]def nice_int(s):
"""
Workaround that int('1.0') raises an exception
@param s: string to be converted to integer
"""
try:
return int(s)
except ValueError:
return int(float(s))
[docs]class StringIO(stringIO.StringIO):
"""
just an interface providing the name and mode property to a StringIO
BugFix for MacOSX mainly
"""
def __init__(self, data, fname=None, mode="r"):
stringIO.StringIO.__init__(self, data)
self.closed = False
if fname == None:
self.name = "fabioStream"
else:
self.name = fname
self.mode = mode
self.lock = threading.Semaphore()
self.__size = None
[docs] def getSize(self):
if self.__size is None:
logger.debug("Measuring size of %s" % self.name)
with self.lock:
pos = self.tell()
self.seek(0, os.SEEK_END)
self.__size = self.tell()
self.seek(pos)
return self.__size
[docs] def setSize(self, size):
self.__size = size
size = property(getSize, setSize)
[docs]class File(file):
"""
wrapper for "file" with locking
"""
def __init__(self, name, mode="rb", buffering=0):
"""file(name[, mode[, buffering]]) -> file object
Open a file. The mode can be 'r', 'w' or 'a' for reading (default),
writing or appending. The file will be created if it doesn't exist
when opened for writing or appending; it will be truncated when
opened for writing. Add a 'b' to the mode for binary files.
Add a '+' to the mode to allow simultaneous reading and writing.
If the buffering argument is given, 0 means unbuffered, 1 means line
buffered, and larger numbers specify the buffer size. The preferred way
to open a file is with the builtin open() function.
Add a 'U' to mode to open the file for input with universal newline
support. Any line ending in the input file will be seen as a '\n'
in Python. Also, a file so opened gains the attribute 'newlines';
the value for this attribute is one of None (no newline read yet),
'\r', '\n', '\r\n' or a tuple containing all the newline types seen.
'U' cannot be combined with 'w' or '+' mode.
"""
file.__init__(self, name, mode, buffering)
self.lock = threading.Semaphore()
self.__size = None
[docs] def getSize(self):
if self.__size is None:
logger.debug("Measuring size of %s" % self.name)
with self.lock:
pos = self.tell()
self.seek(0, os.SEEK_END)
self.__size = self.tell()
self.seek(pos)
return self.__size
[docs] def setSize(self, size):
self.__size = size
def __exit__(self, *args, **kwargs):
"""
Close the file.
"""
return file.close(self)
def __enter__(self, *args, **kwargs):
return self
size = property(getSize, setSize)
[docs]class UnknownCompressedFile(File):
"""
wrapper for "File" with locking
"""
def __init__(self, name, mode="rb", buffering=0):
logger.warning("No decompressor found for this type of file (are gzip anf bz2 installed ???")
File.__init__(self, name, mode, buffering)
if gzip is None:
GzipFile = UnknownCompressedFile
else:
[docs] class GzipFile(gzip.GzipFile):
"""
Just a wrapper forgzip.GzipFile providing the correct seek capabilities for python 2.5
"""
def __init__(self, filename=None, mode=None, compresslevel=9, fileobj=None):
"""
Wrapper with locking for constructor for the GzipFile class.
At least one of fileobj and filename must be given a
non-trivial value.
The new class instance is based on fileobj, which can be a regular
file, a StringIO object, or any other object which simulates a file.
It defaults to None, in which case filename is opened to provide
a file object.
When fileobj is not None, the filename argument is only used to be
included in the gzip file header, which may includes the original
filename of the uncompressed file. It defaults to the filename of
fileobj, if discernible; otherwise, it defaults to the empty string,
and in this case the original filename is not included in the header.
The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', or 'wb',
depending on whether the file will be read or written. The default
is the mode of fileobj if discernible; otherwise, the default is 'rb'.
Be aware that only the 'rb', 'ab', and 'wb' values should be used
for cross-platform portability.
The compresslevel argument is an integer from 1 to 9 controlling the
level of compression; 1 is fastest and produces the least compression,
and 9 is slowest and produces the most compression. The default is 9.
"""
gzip.GzipFile.__init__(self, filename, mode, compresslevel, fileobj)
self.lock = threading.Semaphore()
self.__size = None
# self.getSize()
def __repr__(self):
return "fabio." + gzip.GzipFile.__repr__(self)
[docs] def getSize(self):
if self.mode == gzip.WRITE:
return self.size
if self.__size is None:
with self.lock:
if self.__size is None:
pos = self.offset
end_pos = len(gzip.GzipFile.read(self)) + pos
self.seek(pos)
logger.debug("Measuring size of %s: %s @ %s == %s" % (self.name, end_pos, pos, self.offset))
self.__size = end_pos
return self.__size
if sys.version_info < (2, 7):
def setSize(self, value):
self.__size = value
size = property(getSize, setSize)
@property
def closed(self):
return self.fileobj is None
def seek(self, offset, whence=os.SEEK_SET):
"""
Move to new file position.
Argument offset is a byte count. Optional argument whence defaults to
0 (offset from start of file, offset should be >= 0); other values are 1
(move relative to current position, positive or negative), and 2 (move
relative to end of file, usually negative, although many platforms allow
seeking beyond the end of a file). If the file is opened in text mode,
only offsets returned by tell() are legal. Use of other offsets causes
undefined behavior.
This is a wrapper for seek to ensure compatibility with old python 2.5
Warning: Seek from end is not supported (works only for single blocks !!!)
This implemtents a hack
"""
if whence == os.SEEK_SET:
gzip.GzipFile.seek(self, offset)
elif whence == os.SEEK_CUR:
gzip.GzipFile.seek(self, offset + self.tell())
elif whence == os.SEEK_END:
gzip.GzipFile.seek(self, offset + self.getSize())
def __enter__(self, *args, **kwargs):
return self
def __exit__(self, *args, **kwargs):
"""
Close the file.
"""
return gzip.GzipFile.close(self)
if bz2 is None:
BZ2File = UnknownCompressedFile
else:
[docs] class BZ2File(bz2.BZ2File):
"Wrapper with lock"
def __init__(self, name , mode='r', buffering=0, compresslevel=9):
"""
BZ2File(name [, mode='r', buffering=0, compresslevel=9]) -> file object
Open a bz2 file. The mode can be 'r' or 'w', for reading (default) or
writing. When opened for writing, the file will be created if it doesn't
exist, and truncated otherwise. If the buffering argument is given, 0 means
unbuffered, and larger numbers specify the buffer size. If compresslevel
is given, must be a number between 1 and 9.
Add a 'U' to mode to open the file for input with universal newline
support. Any line ending in the input file will be seen as a '\n' in
Python. Also, a file so opened gains the attribute 'newlines'; the value
for this attribute is one of None (no newline read yet), '\r', '\n',
'\r\n' or a tuple containing all the newline types seen. Universal
newlines are available only when reading.
"""
bz2.BZ2File.__init__(self, name , mode, buffering, compresslevel)
self.lock = threading.Semaphore()
self.__size = None
[docs] def getSize(self):
if self.__size is None:
logger.debug("Measuring size of %s" % self.name)
with self.lock:
pos = self.tell()
all = self.read()
self.__size = self.tell()
self.seek(pos)
return self.__size
[docs] def setSize(self, value):
self.__size = value
size = property(getSize, setSize)
def __exit__(self, *args, **kwargs):
"""
Close the file.
"""
return bz2.BZ2File.close(self)
def __enter__(self, *args, **kwargs):
return self
[docs]class DebugSemaphore(threading._Semaphore):
"""
threading.Semaphore like class with helper for fighting dead-locks
"""
write_lock = threading._Semaphore()
blocked = []
def __init__(self, *arg, **kwarg):
threading._Semaphore.__init__(self, *arg, **kwarg)
[docs] def acquire(self, *arg, **kwarg):
if self._Semaphore__value == 0:
with self.write_lock:
self.blocked.append(id(self))
sys.stderr.write(os.linesep.join(["Blocking sem %s" % id(self)] + \
traceback.format_stack()[:-1] + [""]))
return threading._Semaphore.acquire(self, *arg, **kwarg)
[docs] def release(self, *arg, **kwarg):
with self.write_lock:
uid = id(self)
if uid in self.blocked:
self.blocked.remove(uid)
sys.stderr.write("Released sem %s %s" % (uid, os.linesep))
threading._Semaphore.release(self, *arg, **kwarg)
def __enter__(self):
self.acquire()
return self
def __exit__(self, *arg, **kwarg):
self.release()