# coding: utf-8 # # Project: X-ray image reader # https://github.com/silx-kit/fabio # # Principal author: "Brian R. Pauw" "brian@stack.nl" # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . # """ 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__ = "Brian R. Pauw" __date__ = "02/12/2015" import logging, struct, os import numpy from .fabioimage import FabioImage logger = logging.getLogger("raxisimage") 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.bytecode = 'uint16' # same for all RAXIS images AFAICT self.bpp = 2 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.check_header() # 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 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.warning('special header data type %s not understood' % 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] size = dims[0] * dims[1] * self.bpp if offset >= 0: infile.seek(offset) else: try: attrs = dir(infile) if "measure_size" in attrs: # Handle specifically gzip infile.seek(infile.measure_size() - size) # seek from EOF backwards elif "size" in attrs: infile.seek(infile.size - size) # seek from EOF backwards if "len" in attrs: infile.seek(infile.len - size) # seek from EOF backwards else: infile.seek(-size + offset + 1 , os.SEEK_END) # seek from EOF backwards # infile.seek(-size + offset + 1 , os.SEEK_END) #seek from EOF backwards except IOError as error: logger.warn('expected datablock too large, please check bytecode settings: %s, IOError: %s' % (self.bytecode, error)) except Exception as error: logger.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)) # print(data) 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: %s" % 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 data[di] = (sf * data[di]).astype(numpy.uint32) self.bpp = numpy.dtype(self.bytecode).itemsize 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 raxisimage = RaxisImage