/usr/share/pyshared/fabio/OXDimage.py is in python-fabio 0.0.8-1.
This file is owned by root:root, with mode 0o644.
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"""
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, ESRF
"""
import numpy, logging
logger = logging.getLogger("OXDimage")
from fabioimage import fabioimage
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'}
class OXDimage(fabioimage):
def _readheader(self, infile):
infile.seek(0)
# Ascii header part 512 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['NG'] = int(block[19:26])
#self.header['NK'] = int(block[30:37])
#self.header['NS'] = int(block[41:48])
#self.header['NH'] = int(block[52:59])
block = infile.readline()
#self.header['NSUPPLEMENT'] = int(block[12:19])
block = infile.readline()
self.header['Time'] = block[5:29]
# Skip to general section (NG) 512 byes long <<<<<<"
infile.seek(256)
block = infile.read(512)
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(768)
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(1024)
# Spatial correction file
self.header['Spatial correction file'] = block[26:272]
self.header['Spatial correction file date'] = block[0:26]
# 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)
# calc angles
start_angles_deg = start_angles_step * step2rad * 180.0 / numpy.pi
end_angles_deg = end_angles_step * step2rad * 180.0 / numpy.pi
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]
zero_correction_soft_step = numpy.fromstring(block[512:532], numpy.int32)
zero_correction_soft_deg = zero_correction_soft_step * step2rad * 180.0 / numpy.pi
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(512)
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 - only reads first 256 bytes
block = infile.read(256)
self.header['Flood field image'] = block[99:126]
def read(self, fname):
"""
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
bytecode = numpy.uint8
self.bpp = len(numpy.array(0, bytecode).tostring())
ReadBytes = self.dim1 * self.dim2 * self.bpp
diffs = infile.read(ReadBytes)
diffs = numpy.fromstring(diffs, bytecode)
offset = -127
diffs = diffs.astype(numpy.int32) + offset
if self.header['OI'] > 0:
bytecode = numpy.int16
self.bpp = len(numpy.array(0, bytecode).tostring())
ReadBytes = self.header['OI'] * self.bpp
over_short = infile.read(ReadBytes)
over_short = numpy.fromstring(over_short, bytecode)
if self.header['OL'] > 0:
bytecode = numpy.int32
self.bpp = len(numpy.array(0, bytecode).tostring())
ReadBytes = self.header['OL'] * self.bpp
over_long = infile.read(ReadBytes)
over_long = numpy.fromstring(over_long, bytecode)
block = diffs.copy()
old_val = 0
js = 0
jl = 0
logger.warning('OVER_SHORT: %s', block.dtype)
for i in range(self.dim1 * self.dim2):
if diffs[i] < 127:
#print 'DIFF < 127:' , diffs[i]
d = diffs[i]
elif diffs[i] == 127:
#print 'DIFF == 127:' , diffs[i]
d = over_short[js]
#print 'd ' , d
js = js + 1
elif diffs[i] == 128:
#print 'DIFF == 128:' , diffs[i]
d = over_long[jl]
jl = jl + 1
old_val = old_val + d
block[i] = old_val
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.warning('OVER_SHORT2: %s', block.dtype)
logger.warning("%s" % (block < 0).sum())
#
infile.close()
logger.warning("BYTECODE: %s", bytecode)
try:
# avoid int64 for x86_64 with astype
bytecode = numpy.int32
self.data = numpy.reshape(block.astype(bytecode), [self.dim2, self.dim1])
#self.data = numpy.reshape(block,[self.dim2, self.dim1])
except:
print len(block), self.dim2, self.dim1
raise IOError('Size spec in OD-header does not match size of image data field')
self.bytecode = self.data.dtype.type
self.pilimage = None
return self
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