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replaced deprecated tempfile.mktemp with mkstemp #690

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replaced deprecated tempfile.mktemp with mkstemp #690

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30 changes: 23 additions & 7 deletions cortex/mni.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,11 @@ def compute_mni_transform(subject, xfm,
Transformation matrix from the space specified by `xfm` to MNI space.
"""
# Set up some paths
anat_to_mni_xfm = tempfile.mktemp()
# mkstemp (unlike deprecated mktemp) opens the file itself to avoid a
# race condition; close its fd immediately since only the path is
# needed here (flirt writes to it as an external process).
anat_to_mni_fd, anat_to_mni_xfm = tempfile.mkstemp()
os.close(anat_to_mni_fd)

# Get anatomical image
anat_filename = db.get_anat(subject, "brainmask").get_filename()
Expand Down Expand Up @@ -96,9 +100,15 @@ def transform_to_mni(volumedata, func_to_mni,
`volumedata` after transformation to MNI space.
"""
# Set up paths
func_nii = tempfile.mktemp(".nii.gz")
func_to_mni_xfm = tempfile.mktemp(".mat")
func_in_mni = tempfile.mktemp(".nii.gz")
# mkstemp (unlike deprecated mktemp) opens the file itself to avoid a
# race condition; close its fd immediately since only the path is
# needed here (flirt/nibabel write to it directly).
func_nii_fd, func_nii = tempfile.mkstemp(".nii.gz")
os.close(func_nii_fd)
func_to_mni_xfm_fd, func_to_mni_xfm = tempfile.mkstemp(".mat")
os.close(func_to_mni_xfm_fd)
func_in_mni_fd, func_in_mni = tempfile.mkstemp(".nii.gz")
os.close(func_in_mni_fd)

# Save out relevant things
volumedata.save_nii(func_nii)
Expand Down Expand Up @@ -178,9 +188,15 @@ def transform_mni_to_subject(subject, xfm, volarray, func_to_mni,

"""
# Set up paths
mnispace_func_nii = tempfile.mktemp(".nii.gz")
mni_to_func_xfm = tempfile.mktemp(".mat")
funcspace_nii = tempfile.mktemp(".nii.gz")
# mkstemp (unlike deprecated mktemp) opens the file itself to avoid a
# race condition; close its fd immediately since only the path is
# needed here (flirt/nibabel write to it directly).
mnispace_func_nii_fd, mnispace_func_nii = tempfile.mkstemp(".nii.gz")
os.close(mnispace_func_nii_fd)
mni_to_func_xfm_fd, mni_to_func_xfm = tempfile.mkstemp(".mat")
os.close(mni_to_func_xfm_fd)
funcspace_nii_fd, funcspace_nii = tempfile.mkstemp(".nii.gz")
os.close(funcspace_nii_fd)

# Save out relevant things
affine = nibabel.load(template).affine
Expand Down