fabio.kcdimage — FabIO 0.1.3 documentation

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# Source code for fabio.kcdimage

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

    kcd images are 2D images written by the old KappaCCD diffractometer built by Nonius in the 1990's
    Based on the edfimage.py parser.
    """

    import numpy, logging
    import os, string
    from fabioimage import fabioimage
    logger = logging.getLogger("kcdimage")

    DATA_TYPES = {"u16"  :  numpy.uint16 }

    MINIMUM_KEYS = [
                    'ByteOrder',
                    'Data type',
                    'X dimension',
                    'Y dimension',
                    'Number of readouts']

    DEFAULT_VALUES = { "Data type": "u16" }

    class kcdimage(fabioimage):
        """
        Read the Nonius kcd data format """

        def _readheader(self, infile):
            """
            Read in a header in some KCD format from an already open file
            @
            """
            oneLine = infile.readline()
            alphanum = string.digits + string.letters + ". "
            asciiHeader = True
            for oneChar in oneLine.strip():
                if not oneChar in alphanum:
                    asciiHeader = False

            if asciiHeader is False:
                # This does not look like an edf file
                logger.warning("First line of %s does not seam to be ascii text!" % infile.name)
            endOfHeaders = False
            while not endOfHeaders:
                oneLine = infile.readline()
                if len(oneLine) > 100:
                    endOfHeaders = True
                    break
                if oneLine.strip() == "Binned mode":
                    oneLine = "Mode = Binned"
                try:
                    key, val = oneLine.split('=' , 1)
                except:
                    endOfHeaders = True
                    break
                key = key.strip()
                self.header_keys.append(key)
                self.header[key] = val.strip()
            missing = []
            for item in MINIMUM_KEYS:
                if item not in self.header_keys:
                    missing.append(item)
            if len(missing) > 0:
                logger.debug("KCD file misses the keys " + " ".join(missing))

        def read(self, fname, frame=None):
            """
            Read in header into self.header and
                the data   into self.data
            """
            self.header = {}
            self.resetvals()
            infile = self._open(fname, "rb")
            self._readheader(infile)
            # Compute image size
            try:
                self.dim1 = int(self.header['X dimension'])
                self.dim2 = int(self.header['Y dimension'])
            except:
                raise Exception("KCD file %s is corrupt, cannot read it" % fname)
            try:
                bytecode = DATA_TYPES[self.header['Data type']]
                self.bpp = len(numpy.array(0, bytecode).tostring())
            except KeyError:
                bytecode = numpy.uint16
                self.bpp = 2
                logger.warning("Defaulting type to uint16")
            try:
                nbReadOut = int(self.header['Number of readouts'])
            except KeyError:
                logger.warning("Defaulting number of ReadOut to 1")
                nbReadOut = 1
            fileSize = os.stat(fname)[6]
            expected_size = self.dim1 * self.dim2 * self.bpp * nbReadOut
            infile.seek(fileSize - expected_size)
            block = infile.read()
            assert len(block) == expected_size
            infile.close()

            #now read the data into the array
            self.data = numpy.zeros((self.dim2, self.dim1))
            try:
                for i in range(nbReadOut):
                    self.data += numpy.reshape(numpy.fromstring(
                        block[i * expected_size / nbReadOut:(i + 1) * expected_size / nbReadOut], bytecode),
                        [self.dim2, self.dim1])
            except:
                print len(block), bytecode, self.bpp, self.dim2, self.dim1
                raise IOError, \
                  'Size spec in kcd-header does not match size of image data field'
            self.bytecode = self.data.dtype.type
            self.resetvals()
            # ensure the PIL image is reset
            self.pilimage = None
            return self

        @staticmethod
        def checkData(data=None):
            if data is None:
                return None
            else:
                return data.astype(int)

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