fabio.xsdimage — FabIO 0.1.3 documentation

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# Source code for fabio.xsdimage

    #!/usr/bin/env python
    # coding: utf8
    """
    Authors: Jérôme Kieffer, ESRF
             email:jerome.kieffer@esrf.fr

    XSDimge are XML files containing numpy arrays
    """
    __author__ = "Jérôme Kieffer"
    __contact__ = "jerome.kieffer@esrf.eu"
    __license__ = "GPLv3+"
    __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"

    import logging, numpy
    logger = logging.getLogger("xsdimage")
    from fabioimage import fabioimage
    import base64, hashlib
    try:
        from lxml import etree
    except ImportError:
        logger.warning("lxml library is probably not part of your python installation: disabling xsdimage format")
        etree = None

    class xsdimage(fabioimage):
        """
        Read the XSDataImage XML File data format
        """
        def __init__(self, data=None, header=None, fname=None):
            """
            Constructor of the class XSDataImage.

            @param _strFilename: the name of the file to open
            @type  _strFilename: string
            """
            fabioimage.__init__(self, data=data, header=header)
            self.dims = []
            self.size = None
            self.coding = None
            self.dtype = None
            self.rawData = None
            self.md5 = None
            if fname is not None:
                self.filename = fname
                self.read(fname)

        def read(self, fname, frame=None):
            """
            """
            self.header = {}
            self.resetvals()
            self.filename = fname
            infile = self._open(fname, "rb")
            self._readheader(infile)

            try:
                self.dim1, self.dim2 = self.dims[:2]
            except:
                raise IOError("XSD file %s is corrupt, no dimensions in it" % fname)
            try:
                self.bytecode = numpy.dtype(self.dtype).type
                self.bpp = len(numpy.array(0, self.bytecode).tostring())
            except TypeError:
                self.bytecode = numpy.int32
                self.bpp = 32
                logger.warning("Defaulting type to int32")

            exp_size = 1
            for i in self.dims:
                exp_size *= i
            assert exp_size == self.size

            decData = None
            if self.coding == "base64":
                decData = base64.b64decode(self.rawData)
            elif self.coding == "base32":
                decData = base64.b32decode(self.rawData)
            elif self.coding == "base16":
                decData = base64.b16decode(self.rawData)
            else:
                logger.warning("Unable to recognize the encoding of the data !!! got %s, expected base64, base32 or base16, I assume it is base64 " % self.coding)
                decData = base64.b64decode(self.rawData)
            if self.md5:
                assert  hashlib.md5(decData).hexdigest() == self.md5

            self.data = numpy.fromstring(decData, dtype=self.bytecode).reshape(tuple(self.dims))
            if not numpy.little_endian: #by default little endian
                self.data.byteswap(inplace=True)
            self.resetvals()
    #        # ensure the PIL image is reset
            self.pilimage = None
            return self

        def _readheader(self, infile):
            """
            Read all headers in a file and populate self.header
            data is not yet populated
            @type infile: file object open in read mode
            """
            xml = etree.parse(infile)
            self.dims = []
            for i in xml.xpath("//shape"):
                try:
                    self.dims.append(int(i.text))
                except ValueError, error:
                    logger.warning("%s Shape: Unable to convert %s to integer in %s" % (error, i.text, i))
            for i in xml.xpath("//size"):
                try:
                    self.size = int(i.text)
                except Exception, error:#IGNORE:W0703
                    logger.warning("%s Size: Unable to convert %s to integer in %s" % (error, i.text, i))
            self.dtype = None
            for i in xml.xpath("//dtype"):
                self.dtype = i.text
            self.coding = None
            for i in xml.xpath("//coding"):
                j = i.find("value")
                if j is not None:
                    self.coding = j.text
            self.rawData = None
            for i in xml.xpath("//data"):
                self.rawData = i.text
            self.md5 = None
            for i in xml.xpath("//md5sum"):
                j = i.find("value")
                if j is not None:
                    self.md5 = j.text

    if etree is None:
        xsdimage = None

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