Remove code duplication for function `crop_nifti`

[NicolasGensollen]

The crop_nifti function is currently defined in two places:

clinica/clinica/pipelines/t1_linear/anat_linear_utils.py

Lines 59 to 94 in 81e0586

	def crop_nifti(input_img, ref_crop):
	"""Crop input image based on the reference.
	It uses nilearn `resample_to_img` function.
	Args:
	input_img (str): image to be processed
	ref_crop (str): template used to crop the image
	Returns:
	output_img (NIfTI image): crop image on disk.
	crop_template: (NIfTI image): output template on disk.
	"""
	import os
	from nilearn.image import crop_img, resample_to_img
	basedir = os.getcwd()
	# crop_ref = crop_img(ref_img, rtol=0.5)
	# crop_ref.to_filename(os.path.join(basedir, os.path.basename(input_img).split('.nii')[0] + '_cropped_template.nii.gz'))
	# crop_template = os.path.join(basedir, os.path.basename(input_img).split('.nii')[0] + '_cropped_template.nii.gz')
	# resample the individual MRI into the cropped template image
	crop_img = resample_to_img(input_img, ref_crop, force_resample=True)
	crop_img.to_filename(
	os.path.join(
	basedir, os.path.basename(input_img).split(".nii")[0] + "_cropped.nii.gz"
	)
	)
	output_img = os.path.join(
	basedir, os.path.basename(input_img).split(".nii")[0] + "_cropped.nii.gz"
	)
	crop_template = ref_crop
	return output_img, crop_template

and

clinica/clinica/pipelines/pet_linear/pet_linear_utils.py

Lines 105 to 133 in 81e0586

	def crop_nifti(input_img: str, ref_img: str) -> str:
	"""Crop input image based on the reference.
	It uses nilearn `resample_to_img` function.
	Parameters
	----------
	input_img : str
	Path to the input image.
	ref_img : str
	Path to the reference image used for cropping.
	Returns
	-------
	output_img : str
	Path to the cropped image.
	"""
	from pathlib import Path
	from nilearn.image import resample_to_img
	basedir = Path.cwd()
	# resample the individual MRI into the cropped template image
	crop_img = resample_to_img(input_img, ref_img, force_resample=True)
	crop_filename = Path(input_img.split(".nii")[0] + "_cropped.nii.gz")
	output_img = basedir / crop_filename
	crop_img.to_filename(str(output_img))
	return str(output_img)

By a quick inspection, there are exactly the same except that the later was modernized a bit and that the first one returns both the cropped image and the reference.

It would be great to have a single function with a better signature:

def crop_nifti(input_image: Path, reference_image: Path) -> Path:
    ...

and an adapter task for Nipype:

def crop_nifti_task(input_image: str, reference_image: str) -> str:
    return str(crop_nifti(Path(input_image), Path(reference_image)))

Note: I don't think we need to return the reference as it is one of the inputs. Modifying the connections in the related pipeline should do the trick in my opinion.

I'm not sure where to put these as it will be used by PETLinear and T1Linear. Maybe we could have the function in clinica.utils.image and the adapter within a tasks.py module under clinica.pipelines which defines tasks shared by all pipelines ?

[NicolasGensollen]

I'm reopening because we forgot to add crop_nifti here:

clinica/clinica/utils/image.py

Lines 9 to 14 in 232d335

	__all__ = [
	"compute_aggregated_volume",
	"get_new_image_like",
	"merge_nifti_images_in_time_dimension",
	"remove_dummy_dimension_from_image",
	]

@AliceJoubert could you make a small follow-up PR to add it ?