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BF: Need to read these parameters from file, before getting the data. #615

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merged 3 commits into from
Dec 11, 2020
Merged

BF: Need to read these parameters from file, before getting the data. #615

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d5a5756
BF: Need to read these parameters from file, before getting the data.
arokem Dec 7, 2020
4dfc5d9
NF: Adds mean kurtosis from DKI.
arokem Dec 8, 2020
fbbe73c
Define the MK and AWF properties.
arokem Dec 8, 2020
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41 changes: 39 additions & 2 deletions AFQ/api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -898,7 +898,7 @@ def _dki_md(self, row):
def _dki_awf(self, row, sphere='repulsion100', gtol=1e-2):
dki_awf_file = self._get_fname(row, '_model-DKI_AWF.nii.gz')
if not op.exists(dki_awf_file):
dki_params = self._dki(row).get_fdata()
dki_params = nib.load(self._dki(row)).get_fdata()
awf = axonal_water_fraction(dki_params, sphere=sphere, gtol=gtol)
nib.save(nib.Nifti1Image(awf, row['dwi_affine']),
dki_awf_file)
Expand All @@ -907,12 +907,25 @@ def _dki_awf(self, row, sphere='repulsion100', gtol=1e-2):
afd.write_json(meta_fname, meta)
return dki_awf_file

def _dki_mk(self, row):
dki_mk_file = self._get_fname(row, '_model-DKI_MK.nii.gz')
if not op.exists(dki_mk_file):
tf = self._dki_fit(row)
mk = tf.mk()
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Note that mk is indeed a standard method of the object, and not an attribute (in contrast to fa and md)

nib.save(nib.Nifti1Image(mk, row['dwi_affine']),
dki_mk_file)
meta_fname = self._get_fname(row, '_model-DKI_MK.json')
meta = dict()
afd.write_json(meta_fname, meta)
return dki_mk_file

# Keep track of functions that compute scalars:
_scalar_dict = {"dti_fa": _dti_fa,
"dti_md": _dti_md,
"dki_fa": _dki_fa,
"dki_md": _dki_md,
"dki_awf": _dki_awf}
"dki_awf": _dki_awf,
"dki_mk": _dki_mk}

def _get_best_scalar(self):
for scalar in self.scalars:
Expand Down Expand Up @@ -1810,6 +1823,18 @@ def get_dki(self):

dki = property(get_dki, set_dki)

def set_dki_mk(self):
if 'dki_mk_file' not in self.data_frame.columns:
self.data_frame['dki_mk_file'] =\
self.data_frame.apply(self._dki_mk,
axis=1)

def get_dki_mk(self):
self.set_dki_mk()
return self.data_frame['dki_mk_file']

dki_mk = property(get_dki_mk, set_dki_mk)

def set_dki_fa(self):
if 'dki_fa_file' not in self.data_frame.columns:
self.data_frame['dki_fa_file'] =\
Expand All @@ -1834,6 +1859,18 @@ def get_dki_md(self):

dki_md = property(get_dki_md, set_dki_md)

def set_dki_awf(self):
if 'dki_awf_file' not in self.data_frame.columns:
self.data_frame['dki_awf_file'] =\
self.data_frame.apply(self._dki_awf,
axis=1)

def get_dki_awf(self):
self.set_dki_awf()
return self.data_frame['dki_awf_file']

dki_awf = property(get_dki_awf, set_dki_awf)

def set_mapping(self):
if 'mapping' not in self.data_frame.columns:
self.data_frame['mapping'] =\
Expand Down