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Merged
ste93ste merged 1 commit into from
Dec 18, 2025
Merged

create instance variable 'templateFileName' for class Samseg and Sams… #28

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10 changes: 7 additions & 3 deletions samseg/Samseg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,10 @@ def __init__(self,
raise ValueError('number of mode names does not match number of input images')
self.modeNames = modeNames

self.templateFileName = os.path.join(self.atlasDir, 'template.nii.gz')
if (not os.path.isfile(self.templateFileName)):
self.templateFileName = os.path.join(self.atlasDir, 'template.nii')

# Eugenio: there's a bug in ITK that will cause kvlImage to fail if it contqins the string "recon" ...
# If this problem is not exclusive to the photo mode (RGB), we should move this chunk of code outside the if
# While at it, we also create a grayscale version and a version with a bit of noise around the cerebrum (so the
Expand Down Expand Up @@ -98,7 +102,7 @@ def __init__(self,
# Initialize some objects
self.affine = Affine( imageFileName=self.imageFileNames[0],
meshCollectionFileName=os.path.join(self.atlasDir, 'atlasForAffineRegistration.txt.gz'),
templateFileName=os.path.join(self.atlasDir, 'template.nii.gz' ) )
templateFileName=self.templateFileName )
self.probabilisticAtlas = ProbabilisticAtlas()

# Get full model specifications and optimization options (using default unless overridden by user)
Expand Down Expand Up @@ -323,7 +327,7 @@ def preProcess(self):
else:
self.imageBuffers, self.transform, self.voxelSpacing, self.cropping = readCroppedImages(
self.imageFileNames,
os.path.join(self.atlasDir, 'template.nii.gz'),
self.templateFileName,
self.imageToImageTransformMatrix
)

Expand Down Expand Up @@ -597,7 +601,7 @@ def saveWarpField(self, filename):

# extract geometries
source = sf.load_volume(self.imageFileNames[0]).geom
target = sf.load_volume(os.path.join(self.atlasDir, 'template.nii.gz')).geom
target = sf.load_volume(self.templateFileName).geom

# extract vox-to-vox template transform
# TODO: Grabbing the transform from the saved .mat file in either the cross or base
Expand Down
14 changes: 8 additions & 6 deletions samseg/SamsegLongitudinal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,10 @@ def __init__(self,
for tp in range(self.numberOfTimepoints):
self.tpToBaseTransforms.append(np.eye(4))

self.templateFileName = os.path.join(self.atlasDir, 'template.nii.gz')
if (not os.path.isfile(self.templateFileName)):
self.templateFileName = os.path.join(self.atlasDir, 'template.nii')

# Set image-to-image matrix if provided
self.imageToImageTransformMatrix = imageToImageTransformMatrix

Expand Down Expand Up @@ -209,12 +213,11 @@ def constructAndRegisterSubjectSpecificTemplate(self, initTransformFile=None):
if self.imageToImageTransformMatrix is None:

# Affine atlas registration to sst
templateFileName = os.path.join(self.atlasDir, 'template.nii.gz')
affineRegistrationMeshCollectionFileName = os.path.join(self.atlasDir, 'atlasForAffineRegistration.txt.gz')

affine = Affine(imageFileName=self.sstFileNames[0],
meshCollectionFileName=affineRegistrationMeshCollectionFileName,
templateFileName=templateFileName)
templateFileName=self.templateFileName)
self.imageToImageTransformMatrix, _ = affine.registerAtlas(savePath=sstDir, visualizer=self.visualizer, initTransform=initTransform)


Expand All @@ -229,8 +232,7 @@ def preProcess(self):
#
# =======================================================================================

templateFileName = os.path.join(self.atlasDir, 'template.nii.gz')
self.sstModel.imageBuffers, self.sstModel.transform, self.sstModel.voxelSpacing, self.sstModel.cropping = readCroppedImages(self.sstFileNames, templateFileName, self.imageToImageTransformMatrix)
self.sstModel.imageBuffers, self.sstModel.transform, self.sstModel.voxelSpacing, self.sstModel.cropping = readCroppedImages(self.sstFileNames, self.templateFileName, self.imageToImageTransformMatrix)

self.imageBuffersList = []
self.voxelSpacings = []
Expand All @@ -241,7 +243,7 @@ def preProcess(self):

self.imageBuffersList = []
for imageFileNames in self.imageFileNamesList:
imageBuffers, _, _, _ = readCroppedImages(imageFileNames, templateFileName,
imageBuffers, _, _, _ = readCroppedImages(imageFileNames, self.templateFileName,
self.imageToImageTransformMatrix)
self.imageBuffersList.append(imageBuffers)

Expand Down Expand Up @@ -290,7 +292,7 @@ def preProcess(self):
tmpS = sf.load_volume(os.path.join(self.savePath, "base", "template_coregistered.mgz"))
pToTpTransform = tmpTp.geom.world2vox @ self.tpToBaseTransforms[timepointNumber].inv() @ tmpS.geom.vox2world @ self.imageToImageTransformMatrix

imageBuffers, transform, voxelSpacing, cropping = readCroppedImages(imageFileNames, templateFileName, pToTpTransform.matrix)
imageBuffers, transform, voxelSpacing, cropping = readCroppedImages(imageFileNames, self.templateFileName, pToTpTransform.matrix)

#
self.imageBuffersList.append(imageBuffers)
Expand Down
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