Source code for fabio.openimage

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

"""
import sys, logging
logger = logging.getLogger("openimage")
from fabioutils  import FilenameObject
from fabioimage import fabioimage
import edfimage
import adscimage
import tifimage
import marccdimage
import mar345image
import fit2dmaskimage
import brukerimage
import bruker100image
import pnmimage
import GEimage
import OXDimage
import dm3image
import HiPiCimage
import pilatusimage
import fit2dspreadsheetimage
import kcdimage
import cbfimage
import xsdimage
import binaryimage
import pixiimage
import hdf5image

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')
    ]

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 """
[docs] 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 """
[docs] 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"""
[docs] 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