def get_options(parser):
"""
Command line interface for making a mapping
Add our options to a parser object
"""
parser = ImageD11_file_series.get_options(parser)
parser.add_option("--lookup",
action="store",
type="string",
dest="lookup",
default="None",
help="Lookup tables stem name")
parser.add_option("--outdir",
action="store",
type="string",
dest="outdir",
default=None,
help="Output directory")
parser.add_option("--mask",
action="store",
type="string",
dest="mask",
default=None,
help="fit2d mask file")
return parser
def get_options(parser):
"""
Command line interface for making a mapping
Add our options to a parser object
"""
parser = ImageD11_file_series.get_options( parser )
parser.add_argument("-p", "--pars", action="store",
dest = "pars", default = None,
type=ImageD11options.ParameterFileType(mode='r'),
help = "ImageD11 parameter file for experiment")
parser.add_argument("-o", "--output", action="store",
dest = "output", default = None,
type=ImageD11options.HdfFileType(mode='r'),
help = "Name of hdf5 output file")
parser.add_argument("-s", "--splinefile", action="store",
dest = "spline", default = None,
type=ImageD11options.SplineFileType(mode='r'),
help = "Name of fit2d spline file for spatial dist")
parser.add_argument("-u", "--ubifile", action="store",
dest = "ubifile", default = None,
type = ImageD11options.UbiFileType(mode='r'),
help = "Name of ubi file (first matrix is used)")
parser.add_argument("-x", "--npixels", action="store", type=int,
dest = "npixels", default = 16,
help = "Number of pixels in reciprocal space map per integer hkl [16]")
parser.add_argument("-i", "--images", action="store", type=int,
dest = "images", default = None,
help = "Number of images to process [all]")
parser.add_argument("-b", "--border", action="store", type=int,
dest = "border", default = 10,
help = "Border around images to allocate space, px [10]")
parser.add_argument("-t", "--saturation", action="store", type=float,
dest = "maxpix", default = None,
help = "Saturation value for excluding pixels")
#parser.add_argument("-t", "--testcolfile", action="store", type="string",
# dest = "testcolfile", default=None,
# help = "A columnfile to test geometry")
parser.add_argument("-c", "--subslice", action="store", type=int,
dest = "subslice", default=1,
help = "Number of omega subslices to repeat images")
parser.add_argument("--maskfilename", action="store", type=str,
dest = "maskfilename", default=None,
help = "Mask image (fit2d style)" )
return parser
def main():
"""
A user interface
"""
import sys, time, os, logging
start = time.time()
root = logging.getLogger('')
root.setLevel(logging.WARNING)
try:
from optparse import OptionParser
parser = OptionParser()
parser = get_options(parser)
options, args = parser.parse_args()
except SystemExit:
raise
except:
parser.print_help()
print("\nProblem with your options:")
raise
if options.output is None:
print("You must supply an output file (-o vol.h5)")
sys.exit()
if os.path.exists(options.output):
print("I would overwrite your output file", options.output)
print("If you really want that then delete it first and re-run")
sys.exit()
try:
if options.pars is None:
print("You must supply a parameter file, -p file.pars")
sys.exit()
pars = parameters.parameters()
pars.loadparameters(options.pars)
print("Got parameters from", options.pars)
pd = pars.get_parameters()
names = list(pd.keys())
names.sort()
for name in names:
print("%30s %s" % (name, pd[name]))
except:
print("Problem with parameters:", options.pars)
raise
try:
if options.ubifile is None:
print("You must supply an input ubifile")
ubi = indexing.readubis(options.ubifile)[0]
print("UBI:\n", ubi)
print("Cell parameters:")
print("%.5f %.5f %.5f %.4f %.4f %.4f" % \
indexing.ubitocellpars(ubi))
except:
print("Problem with ubi file:", options.ubifile)
raise
if options.maskfilename is not None:
from fabio.openimage import openimage
try:
mask = (openimage(options.maskfilename).data == 0)
except:
print("Problem with your mask image", options.maskfilename)
raise
print("Using a mask from", options.maskfilename)
print("percent of image used %.3f" %
(100.0 * mask.sum() / mask.shape[0] / mask.shape[1]))
else:
mask = None
first_image = True
nimage = 0
imagefiles = ImageD11_file_series.get_series_from_options(options, args)
print("Subslicing by", options.subslice)
try:
for fim in imagefiles:
if first_image: # allocate volume, compute k etc
first_image = False
mapper = rsv_mapper(fim.data.shape,
pars,
ubi,
options.spline,
np=options.npixels,
border=options.border,
maxpix=options.maxpix,
mask=mask
# FIXME omegarange
)
logging.info("Setting up time %.4f s" % (time.time() - start))
ltp = time.time()
om = float(fim.header['Omega'])
oms = float(fim.header['OmegaStep'])
for i in range(options.subslice):
print(".", end=' ')
omv = om + i * oms / options.subslice
# ==1 : 0*s/1
# ==2 : 0*s/2 , 1*s/2
# ==3 : 0*s/3 , 1*s/3, 2*s/3 etc
mapper.add_image(omv, fim.data)
nimage = nimage + 1
print(" %d %.3f %.4f s, %.4f s" %
(nimage, om, time.time() - ltp, time.time() - start))
if options.images is not None:
if nimage >= options.images:
break
except KeyboardInterrupt:
print("\nCaught a control-c")
if nimage > 0:
print("Problem, trying to save volume so far to:", options.output)
mapper.writevol(options.output)
print("Saved what I had")
sys.exit()
except:
print("\nAn error occured")
if nimage > 0:
print("Problem, trying to save volume so far to:", options.output)
mapper.writevol(options.output)
print("Saved what I had")
raise
if nimage > 0:
mapper.writevol(options.output)
def main():
"""
A CLI user interface
"""
import sys, time, os, logging
start = time.time()
root = logging.getLogger('')
root.setLevel(logging.WARNING)
try:
from optparse import OptionParser
parser = OptionParser()
parser = get_options(parser)
options, args = parser.parse_args()
except SystemExit:
raise
except:
parser.print_help()
print("\nProblem with your options:")
raise
if options.mask is not None:
fit2dmask = (1 - openimage(options.mask).data).ravel()
else:
fit2dmask = 1.0
first_image = True
imagefiles = ImageD11_file_series.get_series_from_options(options, args)
tthvals = numpy.load(options.lookup + "_tth.npy")
try:
for fim in imagefiles:
dataim = fim.data
print(fim.filename)
if first_image: # allocate volume, compute k etc
first_image = False
dxim = openimage(options.lookup + "_dx.edf").data
dyim = openimage(options.lookup + "_dy.edf").data
outsum = numpy.ravel(numpy.zeros(dataim.shape, numpy.float32))
outnp = numpy.ravel(numpy.zeros(dataim.shape, numpy.float32))
e = edfimage()
# C code from rsv_mapper (not intended to be obfuscated)
o = blobcorrector.perfect()
idealx, idealy = o.make_pixel_lut(dataim.shape)
destx, desty = idealx + dxim, idealy + dyim
assert destx.min() >= 0
assert destx.max() < dataim.shape[1]
assert desty.min() >= 0
assert desty.max() < dataim.shape[1]
imageshape = dataim.shape
indices = numpy.ravel(destx).astype(numpy.intp)
numpy.multiply(indices, dataim.shape[1], indices)
numpy.add(indices,
numpy.ravel(desty).astype(numpy.intp), indices)
assert indices.min() >= 0
assert indices.max() < dataim.shape[0] * dataim.shape[1]
on = numpy.ones(len(outnp), numpy.float32)
if fit2dmask is not None:
on = on * fit2dmask
# Number of pixels and mask are constant
cImageD11.put_incr(outnp, indices, on)
mask = outnp < 0.1
scalar = (1.0 - mask) / (outnp + mask)
flatshape = outsum.shape
#
arsorted = mask.copy()
outmask = mask.copy()
outmask = outmask * 1e6
outmask.shape = imageshape
arsorted.shape = imageshape
arsorted.sort(axis=1)
minds = numpy.array([l.searchsorted(0.5) for l in arsorted])
# ENDIF firstimage
start = time.time()
numpy.multiply(outsum, 0, outsum)
outsum.shape = flatshape
dm = (dataim.ravel() * fit2dmask).astype(numpy.float32)
cImageD11.put_incr(outsum, indices, dm)
# outsum = outsum.reshape( dataim.shape )
# outnp = outnp.reshape( dataim.shape ).astype(numpy.int32)
# Normalise
numpy.multiply(outsum, scalar, outsum)
print(dataim.max(), dataim.min(), end=' ')
print(scalar.max(), scalar.min(), outsum.min(), outsum.max())
outsum.shape = imageshape
# saving edf
e.data = outsum
e.write("r_" + fim.filename, force_type=numpy.float32)
print(time.time() - start)
except:
raise