fabio.HiPiCimage — FabIO 0.1.3 documentation

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# Source code for fabio.HiPiCimage

    #!/usr/bin/env python
    """
    Authors: Henning O. Sorensen & Erik Knudsen
             Center for Fundamental Research: Metal Structures in Four Dimensions
             Risoe National Laboratory
             Frederiksborgvej 399
             DK-4000 Roskilde
             email:erik.knudsen@risoe.dk

            + Jon Wright, ESRF

    Information about the file format from Masakatzu Kobayashi is highly appreciated
    """

    import numpy, logging
    logger = logging.getLogger("HiPiCimage")
    from fabioimage import fabioimage

    class HiPiCimage(fabioimage):
        """ Read HiPic images e.g. collected with a Hamamatsu CCD camera"""

        def _readheader(self, infile):
            """
            Read in a header from an already open file

            """
            Image_tag = infile.read(2)
            print Image_tag
            Comment_len = numpy.fromstring(infile.read(2), numpy.uint16)
            Dim_1 = numpy.fromstring(infile.read(2), numpy.uint16)[0]
            Dim_2 = numpy.fromstring(infile.read(2), numpy.uint16)[0]
            Dim_1_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0]
            Dim_2_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0]
            HeaderType = numpy.fromstring(infile.read(2), numpy.uint16)[0]
            Dump = infile.read(50)
            Comment = infile.read(Comment_len)
            self.header['Image_tag'] = Image_tag
            self.header['Dim_1'] = Dim_1
            self.header['Dim_2'] = Dim_2
            self.header['Dim_1_offset'] = Dim_1_offset
            self.header['Dim_2_offset'] = Dim_2_offset
            #self.header['Comment'] = Comment
            if Image_tag != 'IM' :
                # This does not look like an HiPic file
                logging.warning("no opening.  Corrupt header of HiPic file " + \
                                str(infile.name))
            Comment_split = Comment[:Comment.find('\x00')].split('\r\n')

            for topcomment in Comment_split:
                topsplit = topcomment.split(',')
                for line in topsplit:
                    if '=' in line:
                        key, val = line.split('=' , 1)
                        # Users cannot type in significant whitespace
                        key = key.rstrip().lstrip()
                        self.header_keys.append(key)
                        self.header[key] = val.lstrip().rstrip()
                        self.header[key] = val.lstrip('"').rstrip('"')

        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['Dim_1'])
                self.dim2 = int(self.header['Dim_2'])
            except:
                raise Exception("HiPic file", str(fname) + \
                                    "is corrupt, cannot read it")
            bytecode = numpy.uint16
            self.bpp = len(numpy.array(0, bytecode).tostring())

            # Read image data
            block = infile.read(self.dim1 * self.dim2 * self.bpp)
            infile.close()

            #now read the data into the array
            try:
                self.data = numpy.reshape(
                    numpy.fromstring(block, bytecode),
                    [self.dim2, self.dim1])
            except:
                print len(block), bytecode, self.bpp, self.dim2, self.dim1
                raise IOError, \
                  'Size spec in HiPic-header does not match size of image data field'
            self.bytecode = self.data.dtype.type

            # Sometimes these files are not saved as 12 bit,
            # But as 16 bit after bg subtraction - which results
            # negative values saved as 16bit. Therefore values higher
            # 4095 is really negative values
            if self.data.max() > 4095:
                gt12bit = self.data > 4095
                self.data = self.data - gt12bit * (2 ** 16 - 1)

            # ensure the PIL image is reset
            self.pilimage = None
            return self

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