def unit_to_name(self, u):
for name in ('meter', 'mm', 'sec', 'msec', 'usec'):
if u == pimms.unit(name):
return name
# no current support for ppm designation
if u == pimms.unit('um'): return 'micron'
elif u == pimms.unit('1/sec'): return 'hz'
elif u == pimms.unit('Hz'): return 'hz'
elif u == pimms.unit('radian'): return 'rads'
else: return 'unknown'
def test_units(self):
'''
test_units ensures that the various pimms functions related to pint integration work
correctly; these functions include pimms.unit, .mag, .quant, .is_quantity, etc.
'''
# make a few pieces of data with types
x = np.asarray([1.0, 2.0, 3.0, 4.0]) * pimms.units.mm
y = pimms.quant([2, 4, 6, 8], 'sec')
for u in [x, y]:
self.assertTrue(pimms.is_quantity(u))
for u in ('abc', 123, 9.0, []):
self.assertFalse(pimms.is_quantity(u))
for u in [x, y]:
self.assertFalse(pimms.is_quantity(pimms.mag(u)))
self.assertTrue(pimms.like_units(pimms.unit(x), pimms.unit('yards')))
self.assertTrue(pimms.like_units(pimms.unit(y), pimms.unit('minutes')))
self.assertFalse(pimms.like_units(pimms.unit(y), pimms.unit('mm')))
z = x / y
self.assertTrue(pimms.is_vector(x, 'real'))
self.assertTrue(pimms.is_vector(y, 'real'))
self.assertFalse(pimms.is_vector(x, 'int'))
self.assertTrue(pimms.is_vector(y, 'int'))
self.assertTrue(pimms.is_vector(y, 'float'))
self.assertTrue(pimms.is_vector(z, 'real'))
def postprocess_image(self, img, d):
from nibabel.nifti1 import slice_order_codes
hdr = img.header
# dimension information:
for k in ['dimension_information', 'dim_info', 'diminfo']:
try:
hdr.set_dim_info(*d[k])
break
except Exception:
pass
try:
hdr.set_intent(d['intent'])
except Exception:
pass
# xyzt_units:
try:
sunit = self.unit_to_name(pimms.unit(d['voxel_size']))
except Exception:
try:
sunit = self.unit_to_name(pimms.unit(d['voxel_unit']))
except Exception:
sunit = 'unknown'
try:
tunit = self.unit_to_name(pimms.unit(d['slice_duration']))
except Exception:
try:
tunit = self.unit_to_name(pimms.unit(d['time_unit']))
except Exception:
tunit = 'unknown'
try:
hdr.set_xyzt_units(sunit, tunit)
except Exception:
pass
# qform and sform
try:
try:
q = to_affine(d['qform'])
except Exception:
q = to_affine(d['affine'])
qc = d.get('qform_code', None)
hdr.set_qform(q, qc)
except Exception:
pass
try:
try:
s = to_affine(d['sform'])
except Exception:
s = to_affine(d['affine'])
sc = d.get('sform_code', None)
hdr.set_sform(s, sc)
except Exception:
pass
# slice code
try:
hdr['slice_code'] = slice_order_codes[d['slice_order']]
except Exception:
pass
# slice duration
try:
dur = d['slice_duration']
if pimms.is_quantity(dur):
if tunit == 'unknown': dur = pimms.mag(dur)
else: dur = pimms.mag(dur, tunit)
hdr.set_slice_duration(dur)
except Exception:
pass
# slice timing
try:
ts = d['slice_times']
if pimms.is_quantity(ts):
if tunit == 'unknown': ts = pimms.mag(ts)
else: ts = pimms.mag(ts, tunit)
hdr.set_slice_duration([None if np.isnan(t) else t for t in ts])
except Exception:
pass
# slope / intercept
try:
hdr.set_slope_inter(d.get('data_slope', None),
d.get('data_offset', None))
except Exception:
pass
# calibration
try:
(cmn, cmx) = d['calibration']
hdr['cal_min'] = cmn
hdr['cal_max'] = cmx
except Exception:
pass
# time offset
try:
t0 = d['time_offset']
if pimms.is_quantity(t0):
if tunits != 'unknown': t0 = pimms.mag(t0, tunits)
else: t0 = pimms.mag(t0)
hdr['toffset'] = t0
except Exception:
pass
# description
try:
hdr['descrip'] = d['description']
except Exception:
pass
# auxiliary filename
try:
hdr['aux_file'] = d['auxiliary_filename']
except Exception:
pass
return img
