def test_get_regfrom_supplied():
"""
Test a pre-supplied regfrom is preferred to anything else
"""
wsp = get_wsp()
user_regfrom = Image(np.random.rand(5, 5, 5))
wsp.regfrom = user_regfrom
reg.get_regfrom(wsp)
assert (np.allclose(user_regfrom.data, wsp.reg.regfrom.data))
def test_get_regfrom_calib():
"""
Test brain extracted calibration image is used for differenced data
"""
wsp = get_wsp()
wsp.asldata = AslImage(np.random.rand(5, 5, 5, 4),
tis=[1, 2],
iaf="diff",
ibf="rpt")
reg.get_regfrom(wsp)
calib_brain = brain.brain(wsp, wsp.calib, thresh=0.2)
assert (np.allclose(calib_brain.data, wsp.reg.regfrom.data))
def test_get_regfrom_asldata_mean_ct():
"""
Test brain extracted ASL mean is used for CT data
"""
wsp = get_wsp()
wsp.asldata = AslImage(np.random.rand(5, 5, 5, 4),
tis=[1, 2],
iaf="ct",
ibf="rpt")
reg.get_regfrom(wsp)
meanasl_brain = brain.brain(wsp, wsp.asldata.mean(), thresh=0.2)
assert (np.allclose(meanasl_brain.data, wsp.reg.regfrom.data))
def generate_mask(wsp):
"""
Generate mask for ASL data
- If a ready-made mask image is provided or has already been generated, this is returned
- If a structural image is provided this will be used. Brain extraction and registration
will be performed if required
- If a calibration image is provided, this is used. It is assumed to be in the same space
as the ASL data
- If none of the above are present, the ASL data itself is averaged and brain extracted
to produce the mask
Required workspace attributes
-----------------------------
Formally there are no required attributes, however at least one image must be provided
which enables a mask to be generated.
Optional workspace attributes
-----------------------------
- ``asldata`` : ASL data image
- ``mask`` : Existing brain mask
- ``struc`` : Structural image (wholehead)
- ``struc_brain``: Already brain-extracted structural image
- ``asl2struc`` : Existring ASL->Structural space transformation matrix
- ``calib`` : Calibration image
- ``regfrom`` : ASL registration source image
"""
if wsp.rois is not None and wsp.rois.mask is not None:
return
wsp.sub("rois")
# Reporting
page = wsp.report.page("mask")
page.heading("Mask generation", level=0)
if wsp.mask is not None:
wsp.rois.mask_src = "user"
mask_source = "provided by user (assumed to be ASL space): %s" % wsp.mask.name
wsp.rois.mask = wsp.mask
elif wsp.structural.struc is not None:
# Preferred option is to use brain extracted structural
wsp.rois.mask_src = "struc"
struc.init(wsp)
page.heading("Brain extracted structural image", level=1)
page.image(
"struc_brain",
LightboxImage(wsp.structural.brain, bgimage=wsp.structural.struc))
brain_mask_asl = reg.struc2asl(wsp, wsp.structural.brain_mask)
wsp.rois.mask = Image(sp.ndimage.morphology.binary_fill_holes(
(brain_mask_asl.data > 0.25)).astype(np.int),
header=brain_mask_asl.header)
mask_source = "generated from brain extracting structural image and registering to ASL space"
else:
# Alternatively, use registration image (which will be BETed calibration or mean ASL image)
reg.get_regfrom(wsp)
wsp.rois.mask_src = "regfrom"
wsp.rois.mask = Image((wsp.reg.regfrom.data != 0).astype(np.int),
header=wsp.reg.regfrom.header)
mask_source = "generated from brain extracted registration ASL image"
wsp.log.write("\nGenerated ASL data mask\n")
wsp.log.write(" - Mask %s\n" % mask_source)
page.heading("Masked ASL brain image", level=1)
page.text("Mask was %s" % mask_source)
page.text("PW ASL image masked by ASL-space mask")
if wsp.asldata.iaf in ("diff", "tc", "ct"):
page.image(
"mask_outline",
LightboxImage(wsp.rois.mask,
bgimage=wsp.asldata.perf_weighted(),
outline=True))
else:
page.image(
"mask_outline",
LightboxImage(wsp.rois.mask,
bgimage=wsp.asldata.mean(),
outline=True))