from __future__ import absolute_import, division, print_function import re import struct from iotbx.detectors.detectorbase import DetectorImageBase from six.moves import range class MARImage(DetectorImageBase): def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.vendortype = "MARCCD" with open(self.filename,"rb") as fh: byte_order = fh.read(2) if byte_order == b"II": self.endian = 0 else: self.endian = 1 assert not self.isCompressed() def isCompressed(self): if self.getEndian(): format = '>' else: format = '<' with open(self.filename,"rb") as f: f.seek(4) rawdata = f.read(4) ifd = struct.unpack(format+'i',rawdata)[0] # if ifd is 0 then there are no more Image File Directories while ifd: f.seek(ifd) rawdata = f.read(2) # get the number of directory entries in the IFD numentries = struct.unpack(format+'h',rawdata)[0] # search for compression tag for x in range(numentries): f.seek(ifd+x*12+2) rawdata = f.read(2) tag = struct.unpack(format+'h',rawdata)[0] if tag == 259: # value of compression tag f.seek(ifd+x*12+2+8) # seek to value offset # value is left justified in 4 byte field # read two bytes so can unpack as short rawdata = f.read(2) value = struct.unpack(format+'h',rawdata)[0] #print value if value == 1: # no compression return 0 else: return 1 f.seek(ifd+numentries*12+2) rawdata = f.read(4) ifd = struct.unpack(format+'i',rawdata)[0] # control should never reach this point assert False # returns 0 for little endian 'II' # returns 1 for big endian 'MM' def getEndian(self): return self.endian def readHeader(self,offset=1024): if not self.parameters: if self.getEndian(): format = '>' else: format = '<' with open(self.filename, "rb") as f: f.seek(2464) # seek to file_comments file_comments = f.read(512) # read file_comments parameters={} item = (b'Detector Serial Number',b'DETECTOR_SN') #expected integers pattern = re.compile(item[0]+b" = (.*)") matches = pattern.findall(file_comments) if len(matches) > 0: parameters[item[1]] = int(matches[-1]) else: parameters[item[1]] = 0 f.seek(offset+28) rawdata = f.read(8) header_byte_order,data_byte_order = struct.unpack(format+'ii',rawdata) f.seek(offset+80) rawdata = f.read(8) parameters['SIZE1'],parameters['SIZE2'] = struct.unpack(format+'ii',rawdata) assert parameters['SIZE1'] == parameters['SIZE2'] f.seek(offset+88) rawdata = f.read(4) self.depth = struct.unpack(format+'i',rawdata)[0] f.seek(offset+104) rawdata = f.read(4) parameters['CCD_IMAGE_SATURATION'] = struct.unpack(format+'i',rawdata)[0] f.seek(offset+116) rawdata = f.read(12) origin,orientation,view_direction = struct.unpack(format+'iii',rawdata) f.seek(offset+696) rawdata = f.read(4) start_xtal_to_detector = struct.unpack(format+'i',rawdata)[0]/1000. f.seek(offset+728) rawdata = f.read(4) end_xtal_to_detector = struct.unpack(format+'i',rawdata)[0]/1000. #assert start_xtal_to_detector == end_xtal_to_detector #that assertion would've been nice but ESRF BM14 frames fail; instead: #assert the distance is greater than zero in _read_header_asserts parameters['DISTANCE'] = start_xtal_to_detector f.seek(offset+772) rawdata = f.read(8) pixelsize_x,pixelsize_y = struct.unpack(format+'ii',rawdata) assert pixelsize_x == pixelsize_y parameters['PIXEL_SIZE'] = pixelsize_x*1.0e-6 # convert from nano to milli f.seek(offset+644) rawdata = f.read(8) beam_center_x,beam_center_y = struct.unpack(format+'ii',rawdata) parameters['BEAM_CENTER_X'] = beam_center_x/1000.*parameters['PIXEL_SIZE'] parameters['BEAM_CENTER_Y'] = beam_center_y/1000.*parameters['PIXEL_SIZE'] # ----- phi analysis f.seek(offset+684) rawdata = f.read(4) parameters['OSC_START'] = struct.unpack(format+'i',rawdata)[0]/1000. f.seek(offset+716) rawdata = f.read(4) end_phi = struct.unpack(format+'i',rawdata)[0]/1000. #parameters['OSC_RANGE'] = end_phi - parameters['OSC_START'] #would have thought this would work; but turns out unreliable because # software doesn't always fill in the end_phi # ----- rotation analysis f.seek(offset+736) rawdata = f.read(4) rotation_range = struct.unpack(format+'i',rawdata)[0]/1000. parameters['OSC_RANGE'] = rotation_range f.seek(offset+732) rawdata = f.read(4) rotation_axis = struct.unpack(format+'i',rawdata)[0] #assert rotation_axis == 4 # if it isn't phi; go back and recode to cover all cases # ----- omega analysis f.seek(offset+672) rawdata = f.read(4) parameters['OMEGA_START'] = struct.unpack(format+'i',rawdata)[0]/1000. f.seek(offset+704) rawdata = f.read(4) parameters['OMEGA_END'] = struct.unpack(format+'i',rawdata)[0]/1000. if rotation_axis == 4: # rotation axis is phi pass elif rotation_axis == 1: # rotation about omega parameters['OSC_START'] = parameters['OMEGA_START'] f.seek(offset+668) rawdata = f.read(4) start_twotheta = struct.unpack(format+'i',rawdata)[0]/1000. f.seek(offset+700) rawdata = f.read(4) end_twotheta = struct.unpack(format+'i',rawdata)[0]/1000. self._assert_matching_twothetas = start_twotheta == end_twotheta parameters['TWOTHETA'] = start_twotheta f.seek(offset+908) rawdata = f.read(4) parameters['WAVELENGTH'] = struct.unpack(format+'i',rawdata)[0]*1.0e-5 # convert from femto to angstrom self.parameters=parameters self._read_header_asserts() def _read_header_asserts(self): ''' move a couple asserts here that aren't always desireable for un-initialized data ''' assert self.parameters['DISTANCE'] > 0 assert self._assert_matching_twothetas def dataoffset(self): return 4096 def integerdepth(self): return self.depth if __name__=='__main__': i = "/net/racer/scratch1/ttleese/lyso201.0002" #i = "/net/racer/scratch1/ttleese/oxford.tif" m = MARImage(i) print(m.isCompressed()) #m.read() #print 'endian:',m.getEndian() #print 'serial number:',m.serial_number #print 'size 1:',m.size1 #print 'size 2:',m.size2 #print 'npixels:',m.npixels #print 'saturation:',m.saturation #print 'beamx:',m.beamx #print 'beamy:',m.beamy #print 'pixel size:',m.pixel_size #print 'osc start:',m.osc_start #print 'delta phi:',m.deltaphi #print 'two theta:',m.twotheta #print 'wav:',m.wavelength #print 'distance:',m.distance #print 'file length:',m.fileLength()