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Merge pull request #339 from effigies/enh/surface_sphere_project
ENH: Project fsLR mesh onto native sphere to enable single-shot resampling into fsLR
2 parents c06497e + 8361310 commit 0cd77e3

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‎.circleci/ds005_outputs.txt

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smriprep/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt
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smriprep/sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
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smriprep/sub-01/anat/sub-01_hemi-L_curv.shape.gii
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smriprep/sub-01/anat/sub-01_hemi-L_desc-reg_sphere.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-L_inflated.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-L_pial.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-L_smoothwm.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-L_sulc.shape.gii
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smriprep/sub-01/anat/sub-01_hemi-L_thickness.shape.gii
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smriprep/sub-01/anat/sub-01_hemi-L_white.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-R_curv.shape.gii
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smriprep/sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-R_inflated.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-R_pial.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
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smriprep/sub-01/anat/sub-01_hemi-R_sulc.shape.gii
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smriprep/sub-01/anat/sub-01_hemi-R_thickness.shape.gii
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smriprep/sub-01/anat/sub-01_hemi-R_white.surf.gii
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smriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
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smriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
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smriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz

‎docs/conf.py

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apidoc_module_dir = "../smriprep"
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apidoc_output_dir = "api"
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apidoc_excluded_paths = ["conftest.py", "*/tests/*", "tests/*", "data/*", "conf/*"]
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apidoc_excluded_paths = ["conftest.py", "*/conftest.py", "*/tests/*", "tests/*", "data/*", "conf/*"]
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apidoc_separate_modules = True
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apidoc_extra_args = ["--module-first", "-d 1", "-T"]
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‎setup.cfg

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[options]
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python_requires = >=3.8
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install_requires =
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importlib_resources >= 1.3; python_version < '3.9'
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indexed_gzip >= 0.8.8
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lockfile
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looseversion
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[options.package_data]
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smriprep =
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VERSION
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data/boilerplate.bib
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data/io_spec.json
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data/itkIdentityTransform.txt
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data/*
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data/atlases/*
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data/atlases/fs_L/*
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data/atlases/fs_R/*
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interfaces/tests/data/*
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[options.entry_points]
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console_scripts =

‎smriprep/conftest.py

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import os
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from pathlib import Path
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from tempfile import TemporaryDirectory
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import pytest
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os.environ['NO_ET'] = '1'
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@pytest.fixture(autouse=True, scope="session")
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def default_cwd():
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cwd = os.getcwd()
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with TemporaryDirectory(prefix="smriprepTest") as tmpdir:
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try:
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os.chdir(tmpdir)
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yield Path(tmpdir)
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finally:
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os.chdir(cwd)
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@pytest.fixture(autouse=True, scope="session")
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def populate_default_cwd(default_cwd):
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Path.write_bytes(default_cwd / 'lh.white', b'')

‎smriprep/data/__init__.py

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import atexit
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from contextlib import ExitStack
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from pathlib import Path
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try:
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from functools import cache
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except ImportError: # PY38
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from functools import lru_cache as cache
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try: # Prefer backport to leave consistency to dependency spec
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from importlib_resources import files, as_file
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except ImportError:
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from importlib.resources import files, as_file
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__all__ = ["load_resource"]
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exit_stack = ExitStack()
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atexit.register(exit_stack.close)
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path = files(__package__)
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@cache
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def load_resource(fname: str) -> Path:
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return exit_stack.enter_context(as_file(path.joinpath(fname)))

‎smriprep/data/atlases/L.atlasroi.32k_fs_LR.shape.gii

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‎smriprep/data/atlases/R.atlasroi.32k_fs_LR.shape.gii

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‎smriprep/data/atlases/fs_L/fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii

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‎smriprep/data/atlases/fs_L/fsaverage.L.sphere.164k_fs_L.surf.gii

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‎smriprep/data/atlases/fs_R/fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii

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