def parse_options(self):
"""Validate list of parameters.
Raises:
omero_scrits_processing.invalid_parameter
"""
try:
self.options = self.schema(self.options)
except voluptuous.Invalid as e:
raise omero_scripts_processing.invalid_parameter(str(e))
def parse_options(self):
"""Build list of input args to call ndsafir.
Raises:
omero_scripts_processing.invalid_parameter
"""
super(ndsafir, self).parse_options()
## FIXME our version of nd-safir crashes if we don't use time
self.options["time"] = True
try:
self.options = self.schema(self.options)
except voluptuous.Invalid as e:
raise omero_scripts_processing.invalid_parameter(str(e))
## Maximum number of iterations is less when using time
if self.options["time"] and self.options["iterations"] > 5:
raise omero_scripts_processing.invalid_parameter(
"if `time', `iterations' must be less than 6")
opts = [] # list for command line options
## Handle the dimensionality option.
## For 2D and 5D, it is simple but for the other case, we must
## specify the number of dimensions and the dimension type,
## e.g., -4d=zt or -3d=w
dims = ""
for key in ["z-slices", "time", "wavelength"]:
if self.options[key]:
dims += key[0]
ndims = 2 + len(dims)
if ndims == 2:
dopt = "-2d"
elif ndims > 2 and ndims < 5:
dopt = "-%id=%s" % (ndims, dims)
else:
dopt = "-5d"
opts.append(dopt)
## The option value for "gaussian + poisson" is just "poisson"
if self.options["noise_model"] == "gaussian + poisson":
self.options["noise_model"] = "poisson"
## The "sampling" option is a bit trickier because it is optional,
## and its default is patch radius +1.
## XXX: There will be no keys for non-set, optional values, not even
## None, see https://github.com/openmicroscopy/openmicroscopy/issues/2462
if "sampling" not in self.options:
self.options["sampling"] = float(self.options["patch_radius"] +1)
opts += [
"-iter=%i" % (self.options["iterations"]),
"-p=%i" % (self.options["patch_radius"]),
"-noise=%s" % (self.options["noise_model"]),
## FIXME https://github.com/openmicroscopy/openmicroscopy/issues/2449
# "-adapt=%f" % (self.options["adaptability"]),
"-island=%f" % (self.options["island_threshold"]),
"-sampling=%i" % (self.options["sampling"]),
]
self.bin_opts = opts
