def run(self, options):
""" Run the process """
from oxasl import Workspace, calib
from fsl.data.image import Image
data = self.get_data(options)
img = Image(data.raw(), name=data.name)
roi = self.get_roi(options, data.grid)
options["mask"] = Image(roi.raw(), name=roi.name)
calib_name = options.pop("calib-data")
if calib_name not in self.ivm.data:
raise QpException("Calibration data not found: %s" % calib_name)
else:
calib_img = Image(self.ivm.data[calib_name].resample(
data.grid).raw(),
name=calib_name)
ref_roi_name = options.pop("ref-roi", None)
if ref_roi_name is not None:
if ref_roi_name not in self.ivm.rois:
raise QpException("Reference ROI not found: %s" % calib_name)
else:
options["ref_mask"] = Image(
self.ivm.rois[ref_roi_name].resample(data.grid).raw(),
name=ref_roi_name)
options["calib_method"] = options.pop("method", None)
output_name = options.pop("output-name", data.name + "_calib")
logbuf = six.StringIO()
wsp = Workspace(log=logbuf, **options)
wsp.calib = calib_img
## FIXME variance mode
calibrated = calib.calibrate(wsp, img)
self.log(logbuf.getvalue())
self.ivm.add(name=output_name,
data=calibrated.data,
grid=data.grid,
make_current=True)
def get_wsp():
wsp = Workspace(debug=True)
wsp.struc = Image(np.random.rand(10, 10, 10))
wsp.calib = Image(np.random.rand(5, 5, 5))
return wsp
