/usr/lib/python2.7/dist-packages/fabio/OXDimage.py is in python-fabio 0.3.0+dfsg-1build1.
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#
# Project: X-ray image reader
# https://github.com/kif/fabio
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# 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 <http://www.gnu.org/licenses/>.
#
"""
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)
"""
# Get ready for python3:
from __future__ import with_statement, print_function
import time, logging, struct
logger = logging.getLogger("OXDimage")
import numpy
from .fabioimage import FabioImage
from .compression import decTY1, compTY1
from .fabioutils import to_str
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
Note: We assume the binary format is alway little-endian, is this True ?
"""
def _readheader(self, infile):
infile.seek(0)
# Ascii header part 256 byes long
self.header['Header Version'] = to_str(infile.readline()[:-2])
block = infile.readline()
self.header['Compression'] = to_str(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'] = to_str(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'] = struct.unpack("<H", block[0:2])[0]
self.header['Binning in y'] = struct.unpack("<H", block[2:4])[0]
self.header['Detector size x'] = struct.unpack("<H", block[22:24])[0]
self.header['Detector size y'] = struct.unpack("<H", block[24:26])[0]
self.header['Pixels in x'] = struct.unpack("<H", block[26:28])[0]
self.header['Pixels in y'] = struct.unpack("<H", block[28:30])[0]
self.header['No of pixels'] = struct.unpack("<I", block[36:40])[0]
# Speciel section (NS) 768 bytes long
block = infile.read(self.header['Special Section size in Byte'])
self.header['Gain'] = struct.unpack("<d", block[56:64])[0]
self.header['Overflows flag'] = struct.unpack("<h", block[464:466])[0]
self.header['Overflow after remeasure flag'] = struct.unpack("<h", block[466:468])[0]
self.header['Overflow threshold'] = struct.unpack("<i", block[472:476])[0]
self.header['Exposure time in sec'] = struct.unpack("<d", block[480:488])[0]
self.header['Overflow time in sec'] = struct.unpack("<d", block[488:496])[0]
self.header['Monitor counts of raw image 1'] = struct.unpack("<i", block[528:532])[0]
self.header['Monitor counts of raw image 2'] = struct.unpack("<i", block[532:536])[0]
self.header['Monitor counts of overflow raw image 1'] = struct.unpack("<i", block[536:540])[0]
self.header['Monitor counts of overflow raw image 2'] = struct.unpack("<i", block[540:544])[0]
self.header['Unwarping'] = struct.unpack("<i", block[544:548])[0]
self.header['Detector type'] = DETECTOR_TYPES[struct.unpack("<i", block[548:552])[0]]
self.header['Real pixel size x (mm)'] = struct.unpack("<d", block[568:576])[0]
self.header['Real pixel size y (mm)'] = struct.unpack("<d", block[576:584])[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'] = to_str(block[26:272].strip(b"\x00"))
self.header['Spatial correction file date'] = to_str(block[0:26].strip(b"\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)
zero_correction_soft_step = numpy.fromstring(block[512:532], numpy.int32)
if not numpy.little_endian:
start_angles_step.byteswap(True)
end_angles_step.byteswap(True)
step2rad.byteswap(True)
zero_correction_soft_step.byteswap(True)
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_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)'] = struct.unpack("<d", block[552:560])[0]
self.header['Beam rot in deg (e3)'] = struct.unpack("<d", block[560:568])[0]
# Wavelenghts alpha1, alpha2, beta
self.header['Wavelength alpha1'] = struct.unpack("<d", block[568:576])[0]
self.header['Wavelength alpha2'] = struct.unpack("<d", block[576:584])[0]
self.header['Wavelength alpha'] = struct.unpack("<d", block[584:592])[0]
self.header['Wavelength beta'] = struct.unpack("<d", block[592:600])[0]
# Detector tilts around e1,e2,e3 in deg
self.header['Detector tilt e1 in deg'] = struct.unpack("<d", block[640:648])[0]
self.header['Detector tilt e2 in deg'] = struct.unpack("<d", block[648:656])[0]
self.header['Detector tilt e3 in deg'] = struct.unpack("<d", block[656:664])[0]
# Beam center
self.header['Beam center x'] = struct.unpack("<d", block[664:672])[0]
self.header['Beam center y'] = struct.unpack("<d", block[672:680])[0]
# Angle (alpha) between kappa rotation axis and e3 (ideally 50 deg)
self.header['Alpha angle in deg'] = struct.unpack("<d", block[672:680])[0]
# Angle (beta) between phi rotation axis and e3 (ideally 0 deg)
self.header['Beta angle in deg'] = struct.unpack("<d", block[672:680])[0]
# Detector distance
self.header['Distance in mm'] = struct.unpack("<d", block[712:720])[0]
# Statistics section (NS) 512 bytes long
block = infile.read(self.header['Statistic Section in Byte'])
self.header['Stat: Min '] = struct.unpack("<i", block[0:4])[0]
self.header['Stat: Max '] = struct.unpack("<i", block[4:8])[0]
self.header['Stat: Average '] = struct.unpack("<d", block[24:32])[0]
self.header['Stat: Stddev '] = numpy.sqrt(struct.unpack("<d", block[32:40])[0])
self.header['Stat: Skewness '] = struct.unpack("<d", block[40:48])[0]
# History section (NH) 2048 bytes long
block = infile.read(self.header['History Section in Byte'])
self.header['Flood field image'] = to_str(block[99:126].strip(b"\x00"))
def read(self, fname, frame=None):
"""
Read in header into self.header and
the data into self.data
"""
self.header = self.check_header()
self.resetvals()
with self._open(fname) as infile:
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':
logger.debug("# 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)
# endianess is handled at the decompression level
raw_data = decTY1(raw8, raw16, raw32)
bytecode = raw_data.dtype
elif self.header['Compression'] == 'TY5':
logger.warning("# Compressed with the TY5 compression")
bytecode = numpy.int8
self.bpp = 1
raw8 = infile.read(self.dim1 * self.dim2)
raw_data = numpy.fromstring(raw8, bytecode)
if self.header['OI'] > 0:
self.raw16 = infile.read(self.header['OI'] * 2)
else:
self.raw16 = ""
if self.header['OL'] > 0:
self.raw32 = infile.read(self.header['OL'] * 4)
else:
self.raw32 = ""
self.rest = infile.read()
self.blob = raw8 + self.raw16 + self.raw32 + self.rest
raw_data = self.dec_TY5(raw8 + self.raw16 + self.raw32)
else:
bytecode = numpy.int32
self.bpp = len(numpy.array(0, bytecode).tostring())
nbytes = self.dim1 * self.dim2 * self.bpp
raw_data = numpy.fromstring(infile.read(nbytes), bytecode)
# Always assume littel-endian on the disk
if not numpy.little_endian:
raw_data.byteswap(True)
# infile.close()
logger.debug('OVER_SHORT2: %s', raw_data.dtype)
logger.debug("%s" % (raw_data < 0).sum())
logger.debug("BYTECODE: %s", bytecode)
self.data = raw_data.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:
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).encode("ASCII")
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
Only TY1 compressed images is currently possible
@param fname: output filename
"""
datablock8, datablock16, datablock32 = compTY1(self.data)
self.header["OI"] = len(datablock16) / 2
self.header["OL"] = len(datablock32) / 4
self.header["Compression"] = "TY1"
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)
def dec_TY5(self, stream):
"""
Attempt to decode TY5 compression scheme
@param stream: input stream
@return: 1D array with data
"""
array_size = self.dim1 * self.dim2
stream_size = len(stream)
data = numpy.zeros(array_size)
raw = numpy.fromstring(stream, dtype="uint8")
pos_inp = pos_out = current = ex1 = ex2 = 0
while pos_inp < stream_size and pos_out < array_size:
if pos_out % self.dim2 == 0:
last = 0
else:
last = current
value = raw[pos_inp]
if value < 254:
# this is the normal case
# # 1 bytes encode one pixel
current = last + value - 127
pos_inp += 1
elif value == 254:
ex1 += 1
# this is the special case 1:
# if the marker 254 is found the next 2 bytes encode one pixel
value = raw[pos_inp + 1:pos_inp + 3].view("int16")
if not numpy.little_endian:
value = value.byteswap(True)
current = last + value[0]
pos_inp += 3
elif value == 255:
# this is the special case 2:
# if the marker 255 is found the next 4 bytes encode one pixel
ex2 += 1
print('special case 32 bits.')
value = raw[pos_inp + 1:pos_inp + 5].view("int32")
if not numpy.little_endian:
value = value.byteswap(True)
current = last + value[0]
pos_inp += 5
data[pos_out] = current
pos_out += 1
print("Exception encountered: 2:%s, 4:%s" % (ex1, ex2))
return data
OXDimage = OxdImage
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 = bytearray(size)
self._dictSize = {}
def __repr__(self):
return bytes(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)
elif numpy.little_endian:
value = numpy.array(value).astype(dtype).tostring()
else:
value = numpy.array(value).astype(dtype).byteswap().tostring()
self.lstChr[offset:offset + self.getSize(dtype)] = value
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