def testVolume(self):
qpd = NumpyData(self.floats4d, grid=self.grid, name="test")
for idx in range(NVOLS):
self.assertTrue(np.allclose(qpd.volume(idx), self.floats4d[..., idx]))
def run(self, options):
self.debug("Run")
method_name = options.pop("method")
mode = options.pop("mode", "reg")
self._save_transform = options.pop("save-transform", None)
# Registration data. Need to know the reg data grid and number of volumes so progress
# and output data can be interpreted correctly
regdata_name = options.pop("reg", options.pop("data", None))
if not regdata_name:
raise QpException("No registration data specified")
elif regdata_name not in self.ivm.data:
raise QpException("Registration data not found: %s" % regdata_name)
regdata = self.ivm.data[regdata_name]
reg_grid = regdata.grid
reg_data = [
regdata,
]
self._output_name = options.pop(
"output-name", regdata.name + options.get("output-suffix", "_reg"))
# Reference data. Defaults to same as reg data so MoCo can be
# supported as self-registration
refdata_name = options.pop("ref", regdata_name)
ref_data = self.ivm.data[refdata_name]
if ref_data.nvols > 1:
refvol = options.pop("ref-vol", "median")
if refvol == "median":
refidx = int(ref_data.nvols / 2)
elif refvol == "mean":
raise NotImplementedError("Not yet implemented")
else:
refidx = refvol
ref_data = NumpyData(ref_data.volume(refidx), ref_data.grid,
"refdata")
# Additional registration targets can be specified which will be transformed
# in the same way as the main registration data.
#
# Useful for masks defined on an unregistered volume.
add_reg = options.pop(
"add-reg", options.pop("warp-rois", options.pop("warp-roi", ())))
# Handle case where additional registation targets are given as a string
if isinstance(add_reg, six.string_types):
add_reg = (add_reg, )
for name in add_reg:
qpdata = self.ivm.data.get(name, None)
if not qpdata:
self.warn(
"Removing non-existant data set from additional registration list: %s"
% name)
else:
reg_data.append(qpdata.resample(reg_grid, suffix=""))
self.debug("Have %i registration targets" % len(reg_data))
# Function input data must be passed as list of arguments for multiprocessingmethod = get_reg_method(method_name)
options_pass = dict(options)
options.clear()
self.start_bg([method_name, mode, reg_data, ref_data, options_pass])
