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# Source code for fabio.raxisimage

    """

    Authors: Brian R. Pauw
    email:  brian@stack.nl

    Written using information gleaned from the ReadRAXISImage program
    written by T. L. Hendrixson, made available by Rigaku Americas.
    Available at: http://www.rigaku.com/downloads/software/readimage.html

    """

    # Get ready for python3:
    from __future__ import with_statement, print_function, division

    __authors__ = ["Brian R. Pauw"]
    __contact__ = "brian@stack.nl"
    __license__ = "GPLv3+"
    __copyright__ = ""
    __version__ = "23 Nov 2013"
    import logging, struct, os
    import numpy
    from .fabioimage import fabioimage
    logger = logging.getLogger("templateimage")

    class raxisimage(fabioimage):
        """
        FabIO image class to read Rigaku RAXIS image files.
        Write functions are not planned as there are plenty of more suitable
        file formats available for storing detector data.
        In particular, the MSB used in Rigaku files is used in an uncommon way:
        it is used as a *multiply-by* flag rather than a normal image value bit.
        While it is said to multiply by the value specified in the header, there
        is at least one case where this is found not to hold, so YMMV and be careful.

        """
        def __init__(self, *arg, **kwargs):
            """
            Generic constructor
            """
            fabioimage.__init__(self, *arg, **kwargs)
            self.data = None
            self.header = {}
            self.dim1 = self.dim2 = 0
            self.m = self.maxval = self.stddev = self.minval = None
            self.header_keys = self.header.keys()
            self.bytecode = 'uint16' #same for all RAXIS images AFAICT
            self.endianness = '>' #this may be tested for.

        def swap_needed(self):
            """not sure if this function is needed"""
            endian=self.endianness
            #Decide if we need to byteswap
            if (endian == '<' and numpy.little_endian) or (endian == '>' and not numpy.little_endian):
                return False
            if (endian == '>' and numpy.little_endian) or (endian == '<' and not numpy.little_endian):
                return True

        def _readheader(self, infile):
            """
            Read and decode the header of a Rigaku RAXIS image.
            The Rigaku format uses a block of (at least) 1400 bytes for storing
            information. The information has a fixed structure, but endianness
            can be flipped for non-char values. Header items which are not
            capitalised form part of a non-standardized data block and may not
            be accurate.

            TODO: It would be useful to have an automatic endianness test in here.

            @param infile: Opened python file (can be stringIO or bzipped file)
            """
            endianness=self.endianness
            #list of header key to keep the order (when writing)
            RKey,orderList=self.rigakuKeys()
            self.header = {}
            self.header_keys = orderList

            #swapBool=False
            fs=endianness
            minHeaderLength=1400 #from rigaku's def
            #if (numpy.little_endian and endianness=='>'):
            #    swapBool=True
            #file should be open already
            #fh=open(filename,'rb')
            infile.seek(0) #hopefully seeking works.
            rawHead=infile.read(minHeaderLength)
            #fh.close() #don't like open files in case of intermediate crash

            self.header=dict()
            curByte=0
            for key in orderList:
                if isinstance(RKey[key],int):
                    # read a number of bytes, convert to char.
                    #if -1, read remainder of header
                    if RKey[key]==-1:
                        rByte=len(rawHead)-curByte
                        self.header[key]=struct.unpack(fs + str(rByte) + 's',
                                rawHead[curByte : curByte + rByte])[0]
                        curByte+=rByte
                        break

                    rByte=RKey[key]
                    self.header[key]=struct.unpack(fs + str(rByte) + 's',
                            rawHead[curByte : curByte + rByte])[0]
                    curByte+=rByte
                elif RKey[key]=='float':
                    #read a float, 4 bytes
                    rByte=4
                    self.header[key]=struct.unpack(fs + 'f',
                            rawHead[curByte : curByte + rByte])[0]
                    curByte+=rByte
                elif RKey[key]=='long':
                    #read a long, 4 bytes
                    rByte=4
                    self.header[key]=struct.unpack(fs + 'l',
                            rawHead[curByte : curByte + rByte])[0]
                    curByte+=rByte
                else:
                    logging.warn('special header data type {} not understood'
                            .format(Rkey[key]))
                if len(rawHead)==curByte:
                    #"end reached"
                    break

        def read(self, fname, frame=None):
            """
            try to read image
            @param fname: name of the file
            @param frame:
            """

            endianness=self.endianness
            self.resetvals()
            infile = self._open(fname,'rb')
            offset=-1 #read from EOF backward
            try:
                self._readheader(infile)
            except:
                raise

            #we read the required bytes from the end of file, using code
            #lifted from binaryimage
            #read the image data

            self.dim1 = self.header['X Pixels']
            self.dim2 = self.header['Y Pixels']
            self.bytecode = numpy.uint16
            dims = [self.dim2, self.dim1]
            bpp = numpy.dtype(self.bytecode).itemsize
            size = dims[0] * dims[1] * bpp

            if offset >= 0:
                infile.seek(offset)
            else:
                try:
                    infile.seek(-size + offset + 1 , os.SEEK_END) #seek from EOF backwards
                except IOError as error:
                    logging.warn('expected datablock too large, please check bytecode settings: %s, IOError: %s' % (self.bytecode, error))
                except Exception as error:
                    logging.error('Uncommon error encountered when reading file: %s' % error)
            rawData = infile.read(size)
            if  self.swap_needed():
                data = numpy.fromstring(rawData, self.bytecode).byteswap().reshape(tuple(dims))
            else:
                data = numpy.fromstring(rawData, self.bytecode).reshape(tuple(dims))

            di = (data >> 15) != 0  # greater than 2^15
            if di.sum() >= 1:
                # find indices for which we need to do the correction (for which
                # the 16th bit is set):

                logger.debug("Correct for PM", di.sum())
                data = data << 1 >> 1  # reset bit #15 to zero
                self.bytecode = numpy.uint32
                data = data.astype(self.bytecode)
                #Now we do some fixing for Rigaku's refusal to adhere to standards:
                sf = self.header['Photomultiplier Ratio']
                #multiply by the ratio  defined in the header
                data[di] *= sf

            self.data = data

            return self

        def rigakuKeys(self):
            #returns dict of keys and keyLengths
            RKey={
                    'InstrumentType':10,
                    'Version':10,
                    'Crystal Name':20,
                    'Crystal System':12,
                    'A':'float',
                    'B':'float',
                    'C':'float',
                    'Alpha':'float',
                    'Beta':'float',
                    'Gamma':'float',
                    'Space Group':12,
                    'Mosaicity':'float',
                    'Memo':80,
                    'Date':12,
                    'Reserved Space 1':84,
                    'User':20,
                    'Xray Target':4,
                    'Wavelength':'float',
                    'Monochromator':20,
                    'Monochromator 2theta':'float',
                    'Collimator':20,
                    'Filter':4,
                    'Crystal-to-detector Distance':'float',
                    'Generator Voltage':'float',
                    'Generator Current':'float',
                    'Focus':12,
                    'Xray Memo':80,
                    'IP shape':'long', #1= cylindrical, 0=flat. A "long" is overkill.
                    'Oscillation Type':'float', #1=weissenberg. else regular. "float"? really?
                    'Reserved Space 2':56,
                    'Crystal Mount (spindle axis)':4,
                    'Crystal Mount (beam axis)':4,
                    'Phi Datum':'float', #degrees
                    'Phi Oscillation Start':'float', #deg
                    'Phi Oscillation Stop':'float',  #deg
                    'Frame Number':'long',
                    'Exposure Time':'float', #minutes
                    'Direct beam X position':'float', #special, x,y
                    'Direct beam Y position':'float', #special, x,y
                    'Omega Angle':'float', #omega angle
                    'Chi Angle':'float', #omega angle
                    '2Theta Angle':'float', #omega angle
                    'Mu Angle':'float', #omega angle
                    'Image Template':204, #used for storing scan template..
                    'X Pixels':'long',
                    'Y Pixels':'long',
                    'X Pixel Length':'float', #mm
                    'Y Pixel Length':'float', #mm
                    'Record Length':'long',
                    'Total':'long',
                    'Starting Line':'long',
                    'IP Number':'long',
                    'Photomultiplier Ratio':'float',
                    'Fade Time (to start of read)':'float',
                    'Fade Time (to end of read)':'float', #good that they thought of this, but is it applied?
                    'Host Type/Endian':10,
                    'IP Type':10,
                    'Horizontal Scan':'long', #0=left->Right, 1=Rigth->Left
                    'Vertical Scan':'long', #0=down->up, 1=up->down
                    'Front/Back Scan':'long', #0=front, 1=back
                    'Pixel Shift (RAXIS V)':'float',
                    'Even/Odd Intensity Ratio (RAXIS V)':'float',
                    'Magic number':'long', #'RAPID'-specific
                    'Number of Axes':'long',
                    'Goniometer Vector ax.1.1':'float',
                    'Goniometer Vector ax.1.2':'float',
                    'Goniometer Vector ax.1.3':'float',
                    'Goniometer Vector ax.2.1':'float',
                    'Goniometer Vector ax.2.2':'float',
                    'Goniometer Vector ax.2.3':'float',
                    'Goniometer Vector ax.3.1':'float',
                    'Goniometer Vector ax.3.2':'float',
                    'Goniometer Vector ax.3.3':'float',
                    'Goniometer Vector ax.4.1':'float',
                    'Goniometer Vector ax.4.2':'float',
                    'Goniometer Vector ax.4.3':'float',
                    'Goniometer Vector ax.5.1':'float',
                    'Goniometer Vector ax.5.2':'float',
                    'Goniometer Vector ax.5.3':'float',
                    'Goniometer Start ax.1':'float',
                    'Goniometer Start ax.2':'float',
                    'Goniometer Start ax.3':'float',
                    'Goniometer Start ax.4':'float',
                    'Goniometer Start ax.5':'float',
                    'Goniometer End ax.1':'float',
                    'Goniometer End ax.2':'float',
                    'Goniometer End ax.3':'float',
                    'Goniometer End ax.4':'float',
                    'Goniometer End ax.5':'float',
                    'Goniometer Offset ax.1':'float',
                    'Goniometer Offset ax.2':'float',
                    'Goniometer Offset ax.3':'float',
                    'Goniometer Offset ax.4':'float',
                    'Goniometer Offset ax.5':'float',
                    'Goniometer Scan Axis':'long',
                    'Axes Names':40,
                    'file':16,
                    'cmnt':20,
                    'smpl':20,
                    'iext':'long',
                    'reso':'long',
                    'save':'long',
                    'dint':'long',
                    'byte':'long',
                    'init':'long',
                    'ipus':'long',
                    'dexp':'long',
                    'expn':'long',
                    'posx':20,
                    'posy':20,
                    'xray':'long',
                    #more values can be added here
                    'Header Leftovers':-1,
                    }

            #make a list with the items in the right order
            orderList=[
                    'InstrumentType',
                    'Version',
                    'Crystal Name',
                    'Crystal System',
                    'A',
                    'B',
                    'C',
                    'Alpha',
                    'Beta',
                    'Gamma',
                    'Space Group',
                    'Mosaicity',
                    'Memo',
                    'Date',
                    'Reserved Space 1',
                    'User',
                    'Xray Target',
                    'Wavelength',
                    'Monochromator',
                    'Monochromator 2theta',
                    'Collimator',
                    'Filter',
                    'Crystal-to-detector Distance',
                    'Generator Voltage',
                    'Generator Current',
                    'Focus',
                    'Xray Memo',
                    'IP shape',
                    'Oscillation Type',
                    'Reserved Space 2',
                    'Crystal Mount (spindle axis)',
                    'Crystal Mount (beam axis)',
                    'Phi Datum',
                    'Phi Oscillation Start',
                    'Phi Oscillation Stop',
                    'Frame Number',
                    'Exposure Time',
                    'Direct beam X position',
                    'Direct beam Y position',
                    'Omega Angle',
                    'Chi Angle',
                    '2Theta Angle',
                    'Mu Angle',
                    'Image Template',
                    'X Pixels',
                    'Y Pixels',
                    'X Pixel Length',
                    'Y Pixel Length',
                    'Record Length',
                    'Total',
                    'Starting Line',
                    'IP Number',
                    'Photomultiplier Ratio',
                    'Fade Time (to start of read)',
                    'Fade Time (to end of read)',
                    'Host Type/Endian',
                    'IP Type',
                    'Horizontal Scan',
                    'Vertical Scan',
                    'Front/Back Scan',
                    'Pixel Shift (RAXIS V)',
                    'Even/Odd Intensity Ratio (RAXIS V)',
                    'Magic number',
                    'Number of Axes',
                    'Goniometer Vector ax.1.1',
                    'Goniometer Vector ax.1.2',
                    'Goniometer Vector ax.1.3',
                    'Goniometer Vector ax.2.1',
                    'Goniometer Vector ax.2.2',
                    'Goniometer Vector ax.2.3',
                    'Goniometer Vector ax.3.1',
                    'Goniometer Vector ax.3.2',
                    'Goniometer Vector ax.3.3',
                    'Goniometer Vector ax.4.1',
                    'Goniometer Vector ax.4.2',
                    'Goniometer Vector ax.4.3',
                    'Goniometer Vector ax.5.1',
                    'Goniometer Vector ax.5.2',
                    'Goniometer Vector ax.5.3',
                    'Goniometer Start ax.1',
                    'Goniometer Start ax.2',
                    'Goniometer Start ax.3',
                    'Goniometer Start ax.4',
                    'Goniometer Start ax.5',
                    'Goniometer End ax.1',
                    'Goniometer End ax.2',
                    'Goniometer End ax.3',
                    'Goniometer End ax.4',
                    'Goniometer End ax.5',
                    'Goniometer Offset ax.1',
                    'Goniometer Offset ax.2',
                    'Goniometer Offset ax.3',
                    'Goniometer Offset ax.4',
                    'Goniometer Offset ax.5',
                    'Goniometer Scan Axis',
                    'Axes Names',
                    'file',
                    'cmnt',
                    'smpl',
                    'iext',
                    'reso',
                    'save',
                    'dint',
                    'byte',
                    'init',
                    'ipus',
                    'dexp',
                    'expn',
                    'posx',
                    'posy',
                    'xray',
                    'Header Leftovers'
                    ]

            return RKey,orderList

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