/usr/share/pyshared/fabio/openimage.py is in python-fabio 0.1.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions
Risoe National Laboratory
Frederiksborgvej 399
DK-4000 Roskilde
email:henning.sorensen@risoe.dk
mods for fabio by JPW
"""
# Get ready for python3:
from __future__ import with_statement, print_function
import sys, logging
logger = logging.getLogger("openimage")
from fabioutils import FilenameObject
from .fabioimage import fabioimage
from . import edfimage
from . import adscimage
from . import tifimage
from . import marccdimage
from . import mar345image
from . import fit2dmaskimage
from . import brukerimage
from . import bruker100image
from . import pnmimage
from . import GEimage
from . import OXDimage
from . import dm3image
from . import HiPiCimage
from . import pilatusimage
from . import fit2dspreadsheetimage
from . import kcdimage
from . import cbfimage
from . import xsdimage
from . import binaryimage
from . import pixiimage
from . import hdf5image
from . import raxisimage
MAGIC_NUMBERS = [
# "\42\5a" : 'bzipped'
# "\1f\8b" : 'gzipped'
("FORMAT : 86" , 'bruker'),
("\x4d\x4d\x00\x2a" , 'tif') ,
# The marCCD and Pilatus formats are both standard tif with a header
# hopefully these byte patterns are unique for the formats
# If not the image will be read, but the is missing
("\x49\x49\x2a\x00\x08\x00" , 'marccd') ,
("\x49\x49\x2a\x00\x82\x00" , 'pilatus') ,
("\x49\x49\x2a\x00" , 'tif') ,
# ADSC must come before edf
("{\nHEA" , 'adsc'),
("{" , 'edf'),
("\r{" , 'edf'),
("\n{" , 'edf'),
("ADEPT" , 'GE'),
("OD" , 'OXD'),
("IM" , 'HiPiC'),
('\x2d\x04' , 'mar345'),
('\xd2\x04' , 'mar345'),
('\x04\x2d' , 'mar345'), #some machines may need byteswapping
('\x04\xd2' , 'mar345'),
# hint : MASK in 32 bit
('M\x00\x00\x00A\x00\x00\x00S\x00\x00\x00K\x00\x00\x00' , 'fit2dmask') ,
('\x00\x00\x00\x03' , 'dm3'),
("No" , "kcd"),
("<" , "xsd"),
("\n\xb8\x03\x00" , 'pixi'),
("\x89\x48\x44\x46" , 'hdf5'),
("R-AXIS" , 'raxis')
]
URL_PREFIX = {"file:":False, "hdf5:":True, "h5:":True} #Shall we split after the last ":"
def do_magic(byts):
""" Try to interpret the bytes starting the file as a magic number """
for magic, format_type in MAGIC_NUMBERS:
if byts.find(magic) == 0:
return format_type
if 0: # debugging - bruker needed 18 bytes below
logger.debug("m: %s f: %s", magic, format_type)
logger.debug("bytes: %s len(bytes) %s", magic, len(magic))
logger.debug("found: %s", byts.find(magic))
for i in range(len(magic)):
logger.debug("%s %s %s %s ", ord(magic[i]), ord(byts[i]), magic[i], byts[i])
raise Exception("Could not interpret magic string")
def openimage(filename, frame=None):
""" Try to open an image """
if isinstance(filename, FilenameObject):
try:
logger.debug("Attempting to open %s" % (filename.tostring()))
obj = _openimage(filename.tostring())
logger.debug("Attempting to read frame %s from %s" % (frame,
filename.tostring()))
obj = obj.read(filename.tostring(), frame)
except Exception, ex:
# multiframe file
#logger.debug( "DEBUG: multiframe file, start # %d"%(
# filename.num)
logger.debug("Exception %s, trying name %s" % (ex, filename.stem))
obj = _openimage(filename.stem)
logger.debug("Reading frame %s from %s" % (filename.num, filename.stem))
obj.read(filename.stem, frame=filename.num)
else:
logger.debug("Attempting to open %s" % (filename))
obj = _openimage(filename)
logger.debug("Attempting to read frame %s from %s" % (frame, filename))
obj = obj.read(filename, frame)
return obj
def openheader(filename):
""" return only the header"""
obj = _openimage(filename)
obj.readheader(filename)
return obj
def _openimage(filename):
"""
determine which format for a filename
and return appropriate class which can be used for opening the image
"""
lower_filename = filename.lower()
for prefix in URL_PREFIX:
if lower_filename.startswith(prefix):
filename = filename[len(prefix):]
if filename.startswith("//"):
filename = filename[2:]
if URL_PREFIX[prefix]: #process :path[slice,:,:]
if "[" in filename:
filename = filename[:filename.index("[")]
if ":" in filename:
col_split = filename.split(":")
filename = ":".join(col_split[:-1])
try:
imo = fabioimage()
byts = imo._open(filename).read(18)
filetype = do_magic(byts)
if filetype == "marccd" and filename.find("mccd") == -1:
# Cannot see a way around this. Need to find something
# to distinguish mccd from regular tif...
filetype = "tif"
except IOError, error:
logger.error("%s: File probably does not exist", error)
raise error
except:
try:
file_obj = FilenameObject(filename=filename)
if file_obj == None:
raise Exception("Unable to deconstruct filename")
if (file_obj.format is not None) and\
len(file_obj.format) != 1 and \
type(file_obj.format) != type(["list"]):
# one of OXD/ ADSC - should have got in previous
raise Exception("openimage failed on magic bytes & name guess")
filetype = file_obj.format
#UNUSED filenumber = file_obj.num
except Exception, error:
logger.error(error)
import traceback
traceback.print_exc()
raise Exception("Fabio could not identify " + filename)
klass_name = "".join(filetype) + 'image'
module = sys.modules.get("fabio." + klass_name, None)
if module is not None:
if hasattr(module, klass_name):
klass = getattr(module, klass_name)
else:
raise Exception("Module %s has no image class" % module)
else:
raise Exception("Filetype not known %s %s" % (filename, klass_name))
obj = klass()
# skip the read for read header
return obj
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