Source code for fabio.fabioutils

#!/usr/bin/env python
#coding: utf8

"""
General purpose utilities functions for fabio
"""
from __future__ import with_statement
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'],
    '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 extract_filenumber(name): """ extract file number """ fobj = FilenameObject(filename=name) return fobj.num
[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 if sys.version_info < (2, 7): def getSize(self): if self.__size is None: logger.debug("Measuring size of %s" % self.name) with open(self.filename, "rb") as f: f.seek(-4) self.__size = numpy.fromstring(f.read(4), dtype=numpy.uint32) return self.__size 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 """ 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, -1) gzip.GzipFile.seek(self, offset + self.tell()) 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