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Build template: delete temporary files #731

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Nov 15, 2024
Merged

Build template: delete temporary files #731

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23 changes: 18 additions & 5 deletions ants/registration/build_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import numpy as np
import os
import shutil
from tempfile import mktemp

import ants
Expand All @@ -14,6 +15,7 @@ def build_template(
blending_weight=0.75,
weights=None,
useNoRigid=True,
output_dir=None,
**kwargs
):
"""
Expand Down Expand Up @@ -44,6 +46,10 @@ def build_template(
useNoRigid : boolean
equivalent of -y in the script. Template update
step will not use the rigid component if this is True.

output_dir : path
directory name where intermediate transforms are written

kwargs : keyword args
extra arguments passed to ants registration

Expand All @@ -60,6 +66,12 @@ def build_template(
>>> timage = ants.build_template( image_list = ( image, image2, image3 ) ).resample_image( (45,45))
>>> timagew = ants.build_template( image_list = ( image, image2, image3 ), weights = (5,1,1) )
"""
work_dir = mktemp() if output_dir is None else output_dir

def make_outprefix(k: int):
os.makedirs(os.path.join(work_dir, f"img{k:04d}"), exist_ok=True)
return os.path.join(work_dir, f"img{k:04d}", "out")

if "type_of_transform" not in kwargs:
type_of_transform = "SyN"
else:
Expand All @@ -80,7 +92,7 @@ def build_template(
affinelist = []
for k in range(len(image_list)):
w1 = ants.registration(
xavg, image_list[k], type_of_transform=type_of_transform, **kwargs
xavg, image_list[k], type_of_transform=type_of_transform, outprefix=make_outprefix(k), **kwargs
)
L = len(w1["fwdtransforms"])
# affine is the last one
Expand All @@ -99,7 +111,7 @@ def build_template(
avgaffine = ants.average_affine_transform_no_rigid(affinelist)
else:
avgaffine = ants.average_affine_transform(affinelist)
afffn = mktemp(suffix=".mat")
afffn = os.path.join(work_dir, "avgAffine.mat")
ants.write_transform(avgaffine, afffn)

if L == 2:
Expand All @@ -108,17 +120,18 @@ def build_template(
wavg = wavg * wscl
# apply affine to the nonlinear?
# need to save the average
wavgA = ants.apply_transforms(fixed = xavgNew, moving = wavg, imagetype=1, transformlist=afffn, whichtoinvert=[1])
wavgfn = mktemp(suffix=".nii.gz")
wavgA = ants.apply_transforms(fixed=xavgNew, moving=wavg, imagetype=1, transformlist=afffn, whichtoinvert=[1])
wavgfn = os.path.join(work_dir, "avgWarp.nii.gz")
ants.image_write(wavgA, wavgfn)
xavg = ants.apply_transforms(fixed=xavgNew, moving=xavgNew, transformlist=[wavgfn, afffn], whichtoinvert=[0, 1])
else:
xavg = ants.apply_transforms(fixed=xavgNew, moving=xavgNew, transformlist=[afffn], whichtoinvert=[1])

os.remove(afffn)
if blending_weight is not None:
xavg = xavg * blending_weight + ants.iMath(xavg, "Sharpen") * (
1.0 - blending_weight
)

if output_dir is None:
shutil.rmtree(work_dir)
return xavg