fabio.OXDimage — FabIO 0.1.3 documentation

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# Source code for fabio.OXDimage

    #!/usr/bin/env python
    #coding: utf8

    from __future__ import with_statement
    __doc__ = """
    Reads Oxford Diffraction Sapphire 3 images

    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, Jérôme Kieffer & Gaël Goret:
      European Synchrotron Radiation Facility;
      Grenoble (France)

    """

    import time, logging, struct
    logger = logging.getLogger("OXDimage")
    import numpy
    from fabioimage import fabioimage
    from compression import decTY1, compTY1

    try:
        from numpy import rad2deg, deg2rad
    except ImportError: #naive implementation for very old numpy (v1.0.1 on MacOSX from Risoe)
        rad2deg = lambda x: 180.0 * x / numpy.pi
        deg2rad = lambda x: x * numpy.pi / 180.

    DETECTOR_TYPES = {0: 'Sapphire/KM4CCD (1x1: 0.06mm, 2x2: 0.12mm)',
    1: 'Sapphire2-Kodak (1x1: 0.06mm, 2x2: 0.12mm)',
    2: 'Sapphire3-Kodak (1x1: 0.03mm, 2x2: 0.06mm, 4x4: 0.12mm)',
    3: 'Onyx-Kodak (1x1: 0.06mm, 2x2: 0.12mm, 4x4: 0.24mm)',
    4: 'Unknown Oxford diffraction detector'}

    DEFAULT_HEADERS = {'Header Version':  'OD SAPPHIRE  3.0',
                       'Compression': "TY1",
                       'Header Size In Bytes': 5120,
                       "ASCII Section size in Byte": 256,
                       "General Section size in Byte": 512,
                       "Special Section size in Byte": 768,
                       "KM4 Section size in Byte": 1024,
                       "Statistic Section in Byte": 512,
                       "History Section in Byte": 2048,
                       'NSUPPLEMENT':0
                       }

    class OXDimage(fabioimage):
        """
        Oxford Diffraction Sapphire 3 images reader/writer class
        """
        def _readheader(self, infile):

            infile.seek(0)

            # Ascii header part 256 byes long
            self.header['Header Version'] = infile.readline()[:-2]
            block = infile.readline()
            self.header['Compression'] = block[12:15]
            block = infile.readline()
            self.header['NX'] = int(block[3:7])
            self.header['NY'] = int(block[11:15])
            self.header['OI'] = int(block[19:26])
            self.header['OL'] = int(block[30:37])
            block = infile.readline()
            self.header['Header Size In Bytes'] = int(block[8:15])
            self.header['General Section size in Byte'] = int(block[19:26])
            self.header['Special Section size in Byte'] = int(block[30:37])
            self.header['KM4 Section size in Byte'] = int(block[41:48])
            self.header['Statistic Section in Byte'] = int(block[52:59])
            self.header['History Section in Byte'] = int(block[63:])
            block = infile.readline()
            self.header['NSUPPLEMENT'] = int(block[12:19])
            block = infile.readline()
            self.header['Time'] = block[5:29]
            self.header["ASCII Section size in Byte"] = self.header['Header Size In Bytes']\
                                                    - self.header['General Section size in Byte']\
                                                    - self.header['Special Section size in Byte'] \
                                                    - self.header['KM4 Section size in Byte']\
                                                    - self.header['Statistic Section in Byte']\
                                                    - self.header['History Section in Byte']\
            # Skip to general section (NG) 512 byes long <<<<<<"
            infile.seek(self.header["ASCII Section size in Byte"])
            block = infile.read(self.header['General Section size in Byte'])
            self.header['Binning in x'] = numpy.fromstring(block[0:2], numpy.uint16)[0]
            self.header['Binning in y'] = numpy.fromstring(block[2:4], numpy.uint16)[0]
            self.header['Detector size x'] = numpy.fromstring(block[22:24], numpy.uint16)[0]
            self.header['Detector size y'] = numpy.fromstring(block[24:26], numpy.uint16)[0]
            self.header['Pixels in x'] = numpy.fromstring(block[26:28], numpy.uint16)[0]
            self.header['Pixels in y'] = numpy.fromstring(block[28:30], numpy.uint16)[0]
            self.header['No of pixels'] = numpy.fromstring(block[36:40], numpy.uint32)[0]

            # Speciel section (NS) 768 bytes long
            block = infile.read(self.header['Special Section size in Byte'])
            self.header['Gain'] = numpy.fromstring(block[56:64], numpy.float)[0]
            self.header['Overflows flag'] = numpy.fromstring(block[464:466], numpy.int16)[0]
            self.header['Overflow after remeasure flag'] = numpy.fromstring(block[466:468], numpy.int16)[0]
            self.header['Overflow threshold'] = numpy.fromstring(block[472:476], numpy.int32)[0]
            self.header['Exposure time in sec'] = numpy.fromstring(block[480:488], numpy.float)[0]
            self.header['Overflow time in sec'] = numpy.fromstring(block[488:496], numpy.float)[0]
            self.header['Monitor counts of raw image 1'] = numpy.fromstring(block[528:532], numpy.int32)[0]
            self.header['Monitor counts of raw image 2'] = numpy.fromstring(block[532:536], numpy.int32)[0]
            self.header['Monitor counts of overflow raw image 1'] = numpy.fromstring(block[536:540], numpy.int32)[0]
            self.header['Monitor counts of overflow raw image 2'] = numpy.fromstring(block[540:544], numpy.int32)[0]
            self.header['Unwarping'] = numpy.fromstring(block[544:548], numpy.int32)[0]
            self.header['Detector type'] = DETECTOR_TYPES[numpy.fromstring(block[548:552], numpy.int32)[0]]
            self.header['Real pixel size x (mm)'] = numpy.fromstring(block[568:576], numpy.float)[0]
            self.header['Real pixel size y (mm)'] = numpy.fromstring(block[576:584], numpy.float)[0]

            # KM4 goniometer section (NK) 1024 bytes long
            block = infile.read(self.header['KM4 Section size in Byte'])
            # Spatial correction file
            self.header['Spatial correction file'] = block[26:272].strip("\x00")
            self.header['Spatial correction file date'] = block[0:26].strip("\x00")
            # Angles are in steps due to stepper motors - conversion factor RAD
            # angle[0] = omega, angle[1] = theta, angle[2] = kappa, angle[3] = phi,
            start_angles_step = numpy.fromstring(block[284:304], numpy.int32)
            end_angles_step = numpy.fromstring(block[324:344], numpy.int32)
            step2rad = numpy.fromstring(block[368:408], numpy.float)
            step_angles_deg = rad2deg(step2rad)
            # calc angles
            start_angles_deg = start_angles_step * step_angles_deg
            end_angles_deg = end_angles_step * step_angles_deg
            self.header['Omega start in deg'] = start_angles_deg[0]
            self.header['Theta start in deg'] = start_angles_deg[1]
            self.header['Kappa start in deg'] = start_angles_deg[2]
            self.header['Phi start in deg'] = start_angles_deg[3]
            self.header['Omega end in deg'] = end_angles_deg[0]
            self.header['Theta end in deg'] = end_angles_deg[1]
            self.header['Kappa end in deg'] = end_angles_deg[2]
            self.header['Phi end in deg'] = end_angles_deg[3]
            self.header['Omega step in deg'] = step_angles_deg[0]
            self.header['Theta step in deg'] = step_angles_deg[1]
            self.header['Kappa step in deg'] = step_angles_deg[2]
            self.header['Phi step in deg'] = step_angles_deg[3]

            zero_correction_soft_step = numpy.fromstring(block[512:532], numpy.int32)
            zero_correction_soft_deg = zero_correction_soft_step * step_angles_deg
            self.header['Omega zero corr. in deg'] = zero_correction_soft_deg[0]
            self.header['Theta zero corr. in deg'] = zero_correction_soft_deg[1]
            self.header['Kappa zero corr. in deg'] = zero_correction_soft_deg[2]
            self.header['Phi zero corr. in deg'] = zero_correction_soft_deg[3]
            # Beam rotation about e2,e3
            self.header['Beam rot in deg (e2)'] = numpy.fromstring(block[552:560], numpy.float)[0]
            self.header['Beam rot in deg (e3)'] = numpy.fromstring(block[560:568], numpy.float)[0]
            # Wavelenghts alpha1, alpha2, beta
            self.header['Wavelength alpha1'] = numpy.fromstring(block[568:576], numpy.float)[0]
            self.header['Wavelength alpha2'] = numpy.fromstring(block[576:584], numpy.float)[0]
            self.header['Wavelength alpha'] = numpy.fromstring(block[584:592], numpy.float)[0]
            self.header['Wavelength beta'] = numpy.fromstring(block[592:600], numpy.float)[0]

            # Detector tilts around e1,e2,e3 in deg
            self.header['Detector tilt e1 in deg'] = numpy.fromstring(block[640:648], numpy.float)[0]
            self.header['Detector tilt e2 in deg'] = numpy.fromstring(block[648:656], numpy.float)[0]
            self.header['Detector tilt e3 in deg'] = numpy.fromstring(block[656:664], numpy.float)[0]

            # Beam center
            self.header['Beam center x'] = numpy.fromstring(block[664:672], numpy.float)[0]
            self.header['Beam center y'] = numpy.fromstring(block[672:680], numpy.float)[0]
            # Angle (alpha) between kappa rotation axis and e3 (ideally 50 deg)
            self.header['Alpha angle in deg'] = numpy.fromstring(block[672:680], numpy.float)[0]
            # Angle (beta) between phi rotation axis and e3 (ideally 0 deg)
            self.header['Beta angle in deg'] = numpy.fromstring(block[672:680], numpy.float)[0]

            # Detector distance
            self.header['Distance in mm'] = numpy.fromstring(block[712:720], numpy.float)[0]
            # Statistics section (NS) 512 bytes long
            block = infile.read(self.header['Statistic Section in Byte'])
            self.header['Stat: Min '] = numpy.fromstring(block[0:4], numpy.int32)[0]
            self.header['Stat: Max '] = numpy.fromstring(block[4:8], numpy.int32)[0]
            self.header['Stat: Average '] = numpy.fromstring(block[24:32], numpy.float)[0]
            self.header['Stat: Stddev '] = numpy.sqrt(numpy.fromstring(block[32:40], numpy.float)[0])
            self.header['Stat: Skewness '] = numpy.fromstring(block[40:48], numpy.float)[0]

            # History section (NH) 2048 bytes long
            block = infile.read(self.header['History Section in Byte'])
            self.header['Flood field image'] = block[99:126].strip("\x00")

        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)
            self._readheader(infile)

            infile.seek(self.header['Header Size In Bytes'])

            # Compute image size
            try:
                self.dim1 = int(self.header['NX'])
                self.dim2 = int(self.header['NY'])
            except:
                raise Exception("Oxford  file", str(fname) + \
                                    "is corrupt, cannot read it")
            #
            if self.header['Compression'] == 'TY1':
                #Compressed with the KM4CCD compression
                raw8 = infile.read(self.dim1 * self.dim2)
                raw16 = None
                raw32 = None
                if self.header['OI'] > 0:
                    raw16 = infile.read(self.header['OI'] * 2)
                if self.header['OL'] > 0:
                    raw32 = infile.read(self.header['OL'] * 4)
                #DEBUG stuff ...
                self.raw8 = raw8
                self.raw16 = raw16
                self.raw32 = raw32
                #END DEBUG
                block = decTY1(raw8, raw16, raw32)
                bytecode = block.dtype

            else:
                bytecode = numpy.int32
                self.bpp = len(numpy.array(0, bytecode).tostring())
                ReadBytes = self.dim1 * self.dim2 * self.bpp
                block = numpy.fromstring(infile.read(ReadBytes), bytecode)

            logger.debug('OVER_SHORT2: %s', block.dtype)
            logger.debug("%s" % (block < 0).sum())
            infile.close()
            logger.debug("BYTECODE: %s", bytecode)
            self.data = block.reshape((self.dim2, self.dim1))
            self.bytecode = self.data.dtype.type
            self.pilimage = None
            return self

        def _writeheader(self):
            """
            @return a string containing the header for Oxford images
            """
            linesep = "\r\n"
            for key in DEFAULT_HEADERS:
                if key not in self.header_keys:
                    self.header_keys.append(key)
                    self.header[key] = DEFAULT_HEADERS[key]

            if "NX" not in self.header.keys() or "NY" not in self.header.keys():
    			self.header['NX'] = self.dim1
    			self.header['NY'] = self.dim2
            ascii_headers = [self.header['Header Version'],
                           "COMPRESSION=%s (%5.1f)" % (self.header["Compression"], self.getCompressionRatio()),
                           "NX=%4i NY=%4i OI=%7i OL=%7i " % (self.header["NX"], self.header["NY"], self.header["OI"], self.header["OL"]),
                           "NHEADER=%7i NG=%7i NS=%7i NK=%7i NS=%7i NH=%7i" % (self.header['Header Size In Bytes'],
                                                                                     self.header['General Section size in Byte'],
                                                                                     self.header['Special Section size in Byte'],
                                                                                     self.header['KM4 Section size in Byte'],
                                                                                     self.header['Statistic Section in Byte'],
                                                                                     self.header['History Section in Byte']),
                            "NSUPPLEMENT=%7i" % (self.header["NSUPPLEMENT"])]
            if "Time" in self.header:
                ascii_headers.append("TIME=%s" % self.header["Time"])
            else:

                ascii_headers.append("TIME=%s" % time.ctime())

            header = (linesep.join(ascii_headers)).ljust(256)

            NG = Section(self.header['General Section size in Byte'], self.header)
            NG.setData('Binning in x', 0, numpy.uint16)
            NG.setData('Binning in y', 2, numpy.uint16)
            NG.setData('Detector size x', 22, numpy.uint16)
            NG.setData('Detector size y', 24, numpy.uint16)
            NG.setData('Pixels in x', 26, numpy.uint16)
            NG.setData('Pixels in y', 28, numpy.uint16)
            NG.setData('No of pixels', 36, numpy.uint32)
            header += NG.__repr__()

            NS = Section(self.header['Special Section size in Byte'], self.header)
            NS.setData('Gain', 56, numpy.float)
            NS.setData('Overflows flag', 464, numpy.int16)
            NS.setData('Overflow after remeasure flag', 466, numpy.int16)
            NS.setData('Overflow threshold', 472, numpy.int32)
            NS.setData('Exposure time in sec', 480, numpy.float)
            NS.setData('Overflow time in sec', 488, numpy.float)
            NS.setData('Monitor counts of raw image 1', 528, numpy.int32)
            NS.setData('Monitor counts of raw image 2', 532, numpy.int32)
            NS.setData('Monitor counts of overflow raw image 1', 536, numpy.int32)
            NS.setData('Monitor counts of overflow raw image 2', 540, numpy.int32)
            NS.setData('Unwarping', 544, numpy.int32)
            if 'Detector type' in  self.header:
                for key, value in  DETECTOR_TYPES.items():
                    if value == self.header['Detector type']:
                        NS.setData(None, 548, numpy.int32, default=key)
            NS.setData('Real pixel size x (mm)', 568, numpy.float)
            NS.setData('Real pixel size y (mm)', 576, numpy.float)
            header += NS.__repr__()

            KM = Section(self.header['KM4 Section size in Byte'], self.header)
            KM.setData('Spatial correction file date', 0, "|S26")
            KM.setData('Spatial correction file', 26, "|S246")
            # Angles are in steps due to stepper motors - conversion factor RAD
            # angle[0] = omega, angle[1] = theta, angle[2] = kappa, angle[3] = phi,
            if self.header.get('Omega step in deg', None):
                KM.setData(None, 368, numpy.float64, deg2rad(self.header["Omega step in deg"]))
                if self.header.get('Omega start in deg', None):
                    KM.setData(None, 284, numpy.int32, self.header["Omega start in deg"] / self.header["Omega step in deg"])
                if self.header.get('Omega end in deg', None):
                    KM.setData(None, 324, numpy.int32, self.header["Omega end in deg"] / self.header["Omega step in deg"])
                if self.header.get('Omega zero corr. in deg', None):
                    KM.setData(None, 512, numpy.int32, self.header['Omega zero corr. in deg'] / self.header["Omega step in deg"])

            if self.header.get('Theta step in deg', None):
                KM.setData(None, 368 + 8, numpy.float64, deg2rad(self.header["Theta step in deg"]))
                if self.header.get('Theta start in deg', None):
                    KM.setData(None, 284 + 4, numpy.int32, self.header["Theta start in deg"] / self.header["Theta step in deg"])
                if self.header.get('Theta end in deg', None):
                    KM.setData(None, 324 + 4, numpy.int32, self.header["Theta end in deg"] / self.header["Theta step in deg"])
                if self.header.get('Theta zero corr. in deg', None):
                    KM.setData(None, 512 + 4, numpy.int32, self.header['Theta zero corr. in deg'] / self.header["Theta step in deg"])

            if self.header.get('Kappa step in deg', None):
                KM.setData(None, 368 + 16, numpy.float64, deg2rad(self.header["Kappa step in deg"]))
                if self.header.get('Kappa start in deg', None):
                    KM.setData(None, 284 + 8, numpy.int32, self.header["Kappa start in deg"] / self.header["Kappa step in deg"])
                if self.header.get('Kappa end in deg', None):
                    KM.setData(None, 324 + 8, numpy.int32, self.header["Kappa end in deg"] / self.header["Kappa step in deg"])
                if self.header.get('Kappa zero corr. in deg', None):
                    KM.setData(None, 512 + 8, numpy.int32, self.header['Kappa zero corr. in deg'] / self.header["Kappa step in deg"])

            if self.header.get('Phi step in deg', None):
                KM.setData(None, 368 + 24, numpy.float64, deg2rad(self.header["Phi step in deg"]))
                if self.header.get('Phi start in deg', None):
                    KM.setData(None, 284 + 12, numpy.int32, self.header["Phi start in deg"] / self.header["Phi step in deg"])
                if self.header.get('Phi end in deg', None):
                    KM.setData(None, 324 + 12, numpy.int32, self.header["Phi end in deg"] / self.header["Phi step in deg"])
                if self.header.get('Phi zero corr. in deg', None):
                    KM.setData(None, 512 + 12, numpy.int32, self.header['Phi zero corr. in deg'] / self.header["Phi step in deg"])

            # Beam rotation about e2,e3
            KM.setData('Beam rot in deg (e2)', 552, numpy.float64)
            KM.setData('Beam rot in deg (e3)', 560, numpy.float64)
            # Wavelenghts alpha1, alpha2, beta
            KM.setData('Wavelength alpha1', 568, numpy.float64)
            KM.setData('Wavelength alpha2', 576, numpy.float64)
            KM.setData('Wavelength alpha', 584, numpy.float64)
            KM.setData('Wavelength beta', 592, numpy.float64)

            # Detector tilts around e1,e2,e3 in deg
            KM.setData('Detector tilt e1 in deg', 640, numpy.float64)
            KM.setData('Detector tilt e2 in deg', 648, numpy.float64)
            KM.setData('Detector tilt e3 in deg', 656, numpy.float64)

            # Beam center
            KM.setData('Beam center x', 664, numpy.float64)
            KM.setData('Beam center y', 672, numpy.float64)
            # Angle (alpha) between kappa rotation axis and e3 (ideally 50 deg)
            KM.setData('Alpha angle in deg', 672, numpy.float64)
            # Angle (beta) between phi rotation axis and e3 (ideally 0 deg)
            KM.setData('Beta angle in deg', 672, numpy.float64)

            # Detector distance
            KM.setData('Distance in mm', 712, numpy.float64)
            header += KM.__repr__()

            SS = Section(self.header['Statistic Section in Byte'], self.header)
            SS.setData('Stat: Min ', 0, numpy.int32)
            SS.setData('Stat: Max ', 4, numpy.int32)
            SS.setData('Stat: Average ', 24, numpy.float64)
            if self.header.get('Stat: Stddev ', None):
                SS.setData(None, 32, numpy.float64, self.header['Stat: Stddev '] ** 2)
            SS.setData('Stat: Skewness ', 40, numpy.float64)
            header += SS.__repr__()

            HS = Section(self.header['History Section in Byte'], self.header)
            HS.setData('Flood field image', 99, "|S27")
            header += HS.__repr__()

            return header

        def write(self, fname):
            """Write Oxford diffraction images: this is still beta
            @param fname: output filename
            """
            datablock8, datablock16, datablock32 = compTY1(self.data)
            self.header["OI"] = len(datablock16) / 2
            self.header["OL"] = len(datablock32) / 4
            with self._open(fname, mode="wb") as outfile:
                outfile.write(self._writeheader())
                outfile.write(datablock8)
                outfile.write(datablock16)
                outfile.write(datablock32)

        def getCompressionRatio(self):
            "calculate the compression factor obtained vs raw data"
            return 100.0 * (self.data.size + 2 * self.header["OI"] + 4 * self.header["OL"]) / (self.data.size * 4)

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

    class Section(object):
        """
        Small helper class for writing binary headers
        """
        def __init__(self, size, dictHeader):
            """
            @param size: size of the header section in bytes
            @param dictHeader: headers of the image
            """
            self.size = size
            self.header = dictHeader
            self.lstChr = ["\x00"] * size
            self._dictSize = {}
        def __repr__(self):
            return "".join(self.lstChr)

        def getSize(self, dtype):
            if not dtype in self._dictSize:
                self._dictSize[dtype] = len(numpy.zeros(1, dtype=dtype).tostring())
            return self._dictSize[dtype]

        def setData(self, key, offset, dtype, default=None):
            """
            @param offset: int, starting position in the section
            @param key: name of the header key
            @param dtype: type of the data to insert (defines the size!)
            """
            if key in self.header:
                value = self.header[key]
            elif key in DEFAULT_HEADERS:
                value = DEFAULT_HEADERS[key]
            else:
                value = default
            if value is None:
                value = "\x00" * self.getSize(dtype)
            else:
                value = numpy.array(value).astype(dtype).tostring()
            self.lstChr[offset:offset + self.getSize(dtype)] = value

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