/usr/share/pyshared/fabio/mar345image.py is in python-fabio 0.1.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#coding: utf8
"""
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
from .fabioimage import fabioimage
import numpy, struct, time, sys, traceback
import logging
logger = logging.getLogger("mar345image")
from .compression import compPCK, decPCK
class mar345image(fabioimage):
_need_a_real_file = True
def __init__(self, *args, **kwargs):
fabioimage.__init__(self, *args, **kwargs)
self.numhigh = None
self.numpixels = None
def read(self, fname, frame=None):
""" Read a mar345 image"""
self.filename = fname
f = self._open(self.filename, "rb")
self._readheader(f)
if 'compressed' in self.header['Format']:
# self.data = decPCK(f, self.dim1, self.dim2, self.numhigh, version=1)
try:
self.data = decPCK(f, self.dim1, self.dim2)
except Exception, error:
logger.error('%s. importing the mar345_io backend: generate an empty 1x1 picture' % error)
f.close()
self.dim1 = 1
self.dim2 = 1
self.bytecode = numpy.int #
self.data = numpy.resize(numpy.array([0], numpy.int), [1, 1])
return self
else:
logger.error("cannot handle these formats yet " + \
"due to lack of documentation")
return None
self.bytecode = numpy.uint
f.close()
return self
def _readheader(self, infile=None):
""" Read a mar345 image header """
# clip was not used anywhere - commented out
# clip = '\x00'
#using a couple of local variables inside this function
f = infile
h = {}
#header is 4096 bytes long
l = f.read(64)
#the contents of the mar345 header is taken to be as
# described in
# http://www.mar-usa.com/support/downloads/mar345_formats.pdf
#the first 64 bytes are 4-byte integers (but in the CBFlib
# example image it seems to 128 bytes?)
#first 4-byte integer is a marker to check endianness
if struct.unpack("<i", l[0:4])[0] == 1234:
fs = '<i'
else:
fs = '>i'
#image dimensions
self.dim1 = self.dim2 = int(struct.unpack(fs, l[4:8])[0])
#number of high intensity pixels
self.numhigh = struct.unpack(fs, l[2 * 4 : (2 + 1) * 4])[0]
h['NumHigh'] = self.numhigh
#Image format
i = struct.unpack(fs, l[3 * 4 : (3 + 1) * 4])[0]
if i == 1:
h['Format'] = 'compressed'
elif i == 2:
h['Format'] = 'spiral'
else:
h['Format'] = 'compressed'
logger.warning("image format could not be detetermined" + \
"- assuming compressed mar345")
#collection mode
h['Mode'] = {0:'Dose', 1: 'Time'}[struct.unpack(fs, l[4 * 4:(4 + 1) * 4])[0]]
#total number of pixels
self.numpixels = struct.unpack(fs, l[5 * 4:(5 + 1) * 4])[0]
h['NumPixels'] = str(self.numpixels)
#pixel dimensions (length,height) in mm
h['PixelLength'] = struct.unpack(fs, l[6 * 4:(6 + 1) * 4])[0] / 1000.0
h['PixelHeight'] = struct.unpack(fs, l[7 * 4:(7 + 1) * 4])[0] / 1000.0
#x-ray wavelength in AA
h['Wavelength'] = struct.unpack(fs, l[8 * 4:(8 + 1) * 4])[0] / 1000000.0
#used distance
h['Distance'] = struct.unpack(fs, l[9 * 4:(9 + 1) * 4])[0] / 1000.0
#starting and ending phi
h['StartPhi'] = struct.unpack(fs, l[10 * 4:11 * 4])[0] / 1000.0
h['EndPhi'] = struct.unpack(fs, l[11 * 4:12 * 4])[0] / 1000.0
#starting and ending omega
h['StartOmega'] = struct.unpack(fs, l[12 * 4:13 * 4])[0] / 1000.0
h['EndOmega'] = struct.unpack(fs, l[13 * 4:14 * 4])[0] / 1000.0
#Chi and Twotheta angles
h['Chi'] = struct.unpack(fs, l[14 * 4:15 * 4])[0] / 1000.0
h['TwoTheta'] = struct.unpack(fs, l[15 * 4:16 * 4])[0] / 1000.0
#the rest of the header is ascii
# TODO: validate these values against the binaries already read
l = f.read(128)
if not 'mar research' in l:
logger.warning("the string \"mar research\" should be in " + \
"bytes 65-76 of the header but was not")
start = 128
else:
start = l.index('mar research')
f.seek(64 + start)
l = f.read(4096 - start - 64).strip()
for m in l.splitlines():
if m == 'END OF HEADER':
break
n = m.split(' ', 1)
if n[0] == '':
continue
if n[0] in ('PROGRAM', 'DATE', 'SCANNER', 'HIGH', 'MULTIPLIER',
'GAIN', 'WAVELENGTH', 'DISTANCE', 'RESOLUTION',
'CHI', 'TWOTHETA', 'MODE', 'TIME', 'GENERATOR',
'MONOCHROMATOR', 'REMARK'):
logger.debug("reading: %s %s", n[0], n[1])
h[n[0]] = n[1].strip()
continue
if n[0] in ('FORMAT'):
(h['DIM'], h['FORMAT_TYPE'], h['NO_PIXELS']) = n[1].split()
continue
if n[0] in ('PIXEL', 'OFFSET', 'PHI', 'OMEGA', 'COUNTS',
'CENTER', 'INTENSITY', 'HISTOGRAM', 'COLLIMATOR'):
n = m.split()
h.update([(n[0] + '_' + n[j], n[j + 1]) for j in range(1, len(n), 2)])
continue
self.header = h
return h
def write(self, fname):
"""Try to write mar345 file. This is still in beta version.
It uses CCP4 (LGPL) PCK1 algo from JPA"""
headers = self._writeheader()
hotpixels = self._high_intensity_pixel_records()
compressed_stream = compPCK(self.data)
try:
outfile = self._open(fname, mode="wb")
outfile.write(headers)
outfile.write(hotpixels)
outfile.write(compressed_stream)
outfile.close()
except Exception, error:
logger.error("Error in writing file %s: %s" % (fname, error))
def _writeheader(self, linesep="\n", size=4096):#the standard padding does not inclued
"""
@param linesep: end of line separator
@return string/bytes containing the mar345 header
"""
try:
version = sys.modules["fabio"].version
except (KeyError, AttributeError):
version = "0.1.1"
lnsep = len(linesep)
self.header["HIGH"] = str(self.nb_overflow_pixels())
binheader = numpy.zeros(16, "int32")
binheader[:4] = numpy.array([1234, self.dim1, int(self.header["HIGH"]), 1])
binheader[4] = (self.header.get("MODE", "TIME") == "TIME")
binheader[5] = self.dim1 * self.dim2
binheader[6] = int(self.header.get("PIXEL_LENGTH", 1))
binheader[7] = int(self.header.get("PIXEL_HEIGHT", 1))
binheader[8] = int(float(self.header.get("WAVELENGTH", 1)) * 1e6)
binheader[9] = int(float(self.header.get("DISTANCE", 1)) * 1e3)
binheader[10] = int(float(self.header.get("PHI_START", 1)) * 1e3)
binheader[11] = int(float(self.header.get("PHI_END", 1)) * 1e3)
binheader[12] = int(float(self.header.get("OMEGA_START", 1)) * 1e3)
binheader[13] = int(float(self.header.get("OMEGA_END", 1)) * 1e3)
binheader[14] = int(float(self.header.get("CHI", 1)) * 1e3)
binheader[15] = int(float(self.header.get("TWOTHETA", 1)) * 1e3)
lstout = [binheader.tostring() + 'mar research'.ljust(64 - lnsep)]
lstout.append("PROGRAM".ljust(15) + (str(self.header.get("PROGRAM", "FabIO Version %s" % (version))).ljust(49 - lnsep)))
lstout.append("DATE".ljust(15) + (str(self.header.get("DATE", time.ctime()))).ljust(49 - lnsep))
key = "SCANNER"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "FORMAT_TYPE"
if key in self.header:
lstout.append("FORMAT".ljust(15) + ("%s %s %s" % (self.dim1, self.header[key], self.dim1 * self.dim2)).ljust(49 - lnsep))
key = "HIGH"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key1 = "PIXEL_LENGTH"
key2 = "PIXEL_HEIGHT"
if (key1 in self.header) and (key2 in self.header):
lstout.append("PIXEL".ljust(15) + ("LENGTH %s HEIGHT %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key1 = "OFFSET_ROFF"
key2 = "OFFSET_TOFF"
if key1 in self.header and key2 in self.header:
lstout.append("OFFSET".ljust(15) + ("ROFF %s TOFF %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key = "MULTIPLIER"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "GAIN"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "WAVELENGTH"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "DISTANCE"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "RESOLUTION"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key1 = "PHI_START"
key2 = "PHI_END"
key3 = "PHI_OSC"
if (key1 in self.header) and (key2 in self.header) and (key3 in self.header):
lstout.append("PHI".ljust(15) + ("START %s END %s OSC %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
key1 = "OMEGA_START"
key2 = "OMEGA_END"
key3 = "OMEGA_OSC"
if (key1 in self.header) and (key2 in self.header) and (key3 in self.header):
lstout.append("OMEGA".ljust(15) + ("START %s END %s OSC %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
key = "CHI"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "TWOTHETA"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key1 = "CENTER_X"
key2 = "CENTER_Y"
if (key1 in self.header) and (key2 in self.header):
lstout.append("CENTER".ljust(15) + ("X %s Y %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key = "MODE"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "TIME"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key1 = "COUNTS_START"
key2 = "COUNTS_END"
key3 = "COUNTS_NMEAS"
if key1 in self.header and key2 in self.header and key3 in self.header:
lstout.append("COUNTS".ljust(15) + ("START %s END %s NMEAS %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
key1 = "COUNTS_MIN"
key2 = "COUNTS_MAX"
if key1 in self.header and key2 in self.header:
lstout.append("COUNTS".ljust(15) + ("MIN %s MAX %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key1 = "COUNTS_AVE"
key2 = "COUNTS_SIG"
if key1 in self.header and key2 in self.header:
lstout.append("COUNTS".ljust(15) + ("AVE %s SIG %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key1 = "INTENSITY_MIN"
key2 = "INTENSITY_MAX"
key3 = "INTENSITY_AVE"
key4 = "INTENSITY_SIG"
if key1 in self.header and key2 in self.header and key3 in self.header and key4 in self.header:
lstout.append("INTENSITY".ljust(15) + ("MIN %s MAX %s AVE %s SIG %s" % (self.header[key1], self.header[key2], self.header[key3], self.header[key4])).ljust(49 - lnsep))
key1 = "HISTOGRAM_START"
key2 = "HISTOGRAM_END"
key3 = "HISTOGRAM_MAX"
if key1 in self.header and key2 in self.header and key3 in self.header:
lstout.append("HISTOGRAM".ljust(15) + ("START %s END %s MAX %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
key = "GENERATOR"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "MONOCHROMATOR"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key1 = "COLLIMATOR_WIDTH"
key2 = "COLLIMATOR_HEIGHT"
if key1 in self.header and key2 in self.header:
lstout.append("COLLIMATOR".ljust(15) + ("WIDTH %s HEIGHT %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key = "REMARK"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
else:
lstout.append(key.ljust(64 - lnsep))
key = "END OF HEADER"
lstout.append(key)
return linesep.join(lstout).ljust(size)
def _high_intensity_pixel_records(self):
flt_data = self.data.flatten()
pix_location = numpy.where(flt_data > 65535)[0]
nb_pix = pix_location.size
if nb_pix % 8 == 0:
tmp = numpy.zeros((nb_pix, 2), dtype="int32")
else:
tmp = numpy.zeros(((nb_pix // 8 + 1) * 8, 2), dtype="int32")
tmp[:nb_pix, 0] = pix_location + 1
tmp[:nb_pix, 1] = flt_data[pix_location]
return tmp.tostring()
def nb_overflow_pixels(self):
return (self.data > 65535).sum()
@staticmethod
def checkData(data=None):
if data is None:
return None
else:
# enforce square image
shape = data.shape
assert len(shape) == 2, "image has 2 dimensions"
mshape = max(shape)
z = numpy.zeros((mshape, mshape), dtype=int)
z[:shape[0], :shape[1]] = data
return z
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