sdcflows 2.5.2__tar.gz → 2.6.0__tar.gz

{sdcflows-2.5.2 → sdcflows-2.6.0}/.maint/MAINTAINERS.md

@@ -12,4 +12,3 @@ If you are participating because of your affiliation with another organization (
 | Esteban | Oscar | @oesteban | 0000-0001-8435-6191 | Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland |
 | Goncalves | Mathias | @mgxd | 0000-0002-7252-7771 | Department of Psychology, Stanford University, CA, USA |
 | Markiewicz | Christopher J. | @effigies | 0000-0002-6533-164X | Department of Psychology, Stanford University, CA, USA |
-

{sdcflows-2.5.2 → sdcflows-2.6.0}/.maint/PIs.md

@@ -14,4 +14,3 @@ If you are participating because of your affiliation with another organization (
 | Poldrack | Russell A. | @poldrack | 0000-0001-6755-0259 | Department of Psychology, Stanford University, CA, USA |
 | Satterthwaite | Theodore D. |  | 0000-0001-7072-9399 | Perelman School of Medicine, University of Pennsylvania, PA, USA |
 | Gorgolewski | Krzysztof J. | @chrisgorgo | 0000-0003-3321-7583 | Google LLC |
-

{sdcflows-2.5.2 → sdcflows-2.6.0}/CHANGES.rst

@@ -1,3 +1,27 @@
+2.6.0 (November 10, 2023)
+=========================
+New feature release in the 2.6.0 series.
+
+This release resolves a number of issues with fieldmaps inducing distortions
+during correction. Phase difference and direct fieldmaps are now masked correctly,
+preventing the overestimation of distortions outside the brain. Additionally,
+we now implement Jacobian weighting during unwarping, which corrects for compression
+and expansion effects on signal intensity.
+
+* FIX: Mask fieldmap before fitting spline field (#396)
+* FIX: Interpolate to floating point values (#394)
+* FIX: Refactoring the ``B0FieldTransform`` implementation (#346)
+* FIX: Nipype workflows like to be passed absolute paths (phasediff fieldmap) (#374)
+* ENH: Implement Jacobian weighting during unwarp (#391)
+* ENH: Output target2fmap_xfm from coeff2epi_wf (#381)
+* ENH: Add data loader to sdcflows.data, drop pkg_resources (#379)
+* RF: Use scipy.interpolate.BSpline to construct spline basis (#393)
+* DOC: Use latest sphinx to fix bad sphinx/furo interaction (#390)
+* DOC: Fix missing dependency when merging new data loader (#380)
+* MNT: Update emprical values in test to allow transition to new scipy's BSpline (#387)
+* MNT: Add pre-commit config (#375)
+* MNT: Add a seed to random generator of coefficients (#368)
+
 2.5.2 (November 09, 2023)
 =========================
 Bug-fix release in the 2.5.x series.

{sdcflows-2.5.2 → sdcflows-2.6.0}/Makefile

@@ -15,4 +15,3 @@ docker:
 	--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
 	--build-arg VCS_REF=`git rev-parse --short HEAD` \
 	--build-arg VERSION=`python setup.py --version` .
-

{sdcflows-2.5.2 → sdcflows-2.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: sdcflows
-Version: 2.5.2
+Version: 2.6.0
 Summary: Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes.
 Home-page: https://www.nipreps.org/sdcflows
 Author: The SDCflows developers
@@ -9,22 +9,25 @@ License: Apache-2.0
 Project-URL: Documentation, https://www.nipreps.org/sdcflows
 Project-URL: GitHub, https://github.com/nipreps/sdcflows
 Project-URL: fMRIPrep, https://fmriprep.readthedocs.io
-Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.8
 Description-Content-Type: text/x-rst; charset=UTF-8
 License-File: LICENSE
 Requires-Dist: attrs>=20.1.0
+Requires-Dist: importlib_resources>=5.7; python_version < "3.11"
 Requires-Dist: nibabel>=3.1.0
 Requires-Dist: nipype<2.0,>=1.8.5
 Requires-Dist: traits<6.4
 Requires-Dist: niworkflows>=1.7.0
-Requires-Dist: nitransforms>=21.0.0
+Requires-Dist: nitransforms>=23.0.1
 Requires-Dist: numpy>=1.21.0
 Requires-Dist: pybids>=0.15.1
 Requires-Dist: scikit-image>=0.18
@@ -87,7 +90,7 @@ SDCFlows
 .. image:: https://github.com/nipreps/sdcflows/workflows/Deps%20&%20CI/badge.svg
     :target: https://github.com/nipreps/sdcflows/actions
 
-SDCFlows (*Susceptibility Distortion Correction workFlows*) is a Python library of 
+SDCFlows (*Susceptibility Distortion Correction workFlows*) is a Python library of
 *NiPype*-based workflows to preprocess *B0* mapping data, estimate the corresponding
 fieldmap and finally correct for susceptibility distortions.
 Susceptibility-derived distortions are typically displayed by images acquired with EPI

{sdcflows-2.5.2 → sdcflows-2.6.0}/README.rst

@@ -13,7 +13,7 @@ SDCFlows
 .. image:: https://github.com/nipreps/sdcflows/workflows/Deps%20&%20CI/badge.svg
     :target: https://github.com/nipreps/sdcflows/actions
 
-SDCFlows (*Susceptibility Distortion Correction workFlows*) is a Python library of 
+SDCFlows (*Susceptibility Distortion Correction workFlows*) is a Python library of
 *NiPype*-based workflows to preprocess *B0* mapping data, estimate the corresponding
 fieldmap and finally correct for susceptibility distortions.
 Susceptibility-derived distortions are typically displayed by images acquired with EPI

sdcflows-2.6.0/env.yml

@@ -0,0 +1,25 @@
+name: sdcflows
+channels:
+  - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
+  - conda-forge
+# Update this ~yearly; last updated April 2023
+dependencies:
+  - python=3.10
+  # Intel Math Kernel Library for numpy
+  - mkl=2022.1
+  - mkl-service=2.4
+  # Base scientific python stack; required by FSL, so pinned here
+  - numpy=1.26
+  - scipy=1.11
+  - matplotlib=3.8
+  - pandas=2.1
+  - h5py=3.8
+  # Dependencies compiled against numpy, best to stick with conda
+  - scikit-image=0.22
+  # Utilities
+  - graphviz=6.0
+  # Workflow dependencies: ANTs
+  - ants=2.4.4
+  # Workflow dependencies: FSL (versions pinned in 6.0.6.2)
+  - fsl-fugue=2201.2
+  - fsl-topup=2203.1

{sdcflows-2.5.2 → sdcflows-2.6.0}/min-requirements.txt

@@ -1,10 +1,11 @@
 # Auto-generated by .maint/update_requirements.py
 attrs==20.1.0
+importlib_resources==5.7; python_version < "3.11"
 nibabel==3.1.0
 nipype==1.8.5
 traits<6.4
 niworkflows==1.7.0
-nitransforms==21.0.0
+nitransforms==23.0.1
 numpy==1.21.0
 pybids==0.15.1
 scikit-image==0.18

{sdcflows-2.5.2 → sdcflows-2.6.0}/requirements.txt

@@ -1,10 +1,11 @@
 # Auto-generated by .maint/update_requirements.py
 attrs>=20.1.0
+importlib_resources>=5.7; python_version < "3.11"
 nibabel>=3.1.0
 nipype<2.0,>=1.8.5
 traits<6.4
 niworkflows>=1.7.0
-nitransforms>=21.0.0
+nitransforms>=23.0.1
 numpy>=1.21.0
 pybids>=0.15.1
 scikit-image>=0.18

{sdcflows-2.5.2 → sdcflows-2.6.0}/sdcflows/__init__.py

@@ -4,11 +4,10 @@ __copyright__ = "2022, The NiPreps developers"
 try:
     from ._version import __version__
 except ModuleNotFoundError:
-    from pkg_resources import get_distribution, DistributionNotFound
-
+    from importlib.metadata import version, PackageNotFoundError
     try:
-        __version__ = get_distribution(__packagename__).version
-    except DistributionNotFound:
+        __version__ = version(__packagename__)
+    except PackageNotFoundError:
         __version__ = "0+unknown"
-    del get_distribution
-    del DistributionNotFound
+    del version
+    del PackageNotFoundError

{sdcflows-2.5.2 → sdcflows-2.6.0}/sdcflows/_version.py

@@ -1,2 +1,2 @@
 """Version file, automatically generated by setuptools_scm."""
-__version__ = "2.5.2"
+__version__ = "2.6.0"

sdcflows-2.6.0/sdcflows/data/__init__.py

@@ -0,0 +1,182 @@
+"""SDCFlows data files
+
+.. autofunction:: load
+
+.. automethod:: load.readable
+
+.. automethod:: load.as_path
+
+.. automethod:: load.cached
+
+.. autoclass:: Loader
+"""
+from __future__ import annotations
+
+import atexit
+import os
+from contextlib import AbstractContextManager, ExitStack
+from functools import cached_property
+from pathlib import Path
+from types import ModuleType
+from typing import Union
+
+try:
+    from functools import cache
+except ImportError:  # PY38
+    from functools import lru_cache as cache
+
+try:  # Prefer backport to leave consistency to dependency spec
+    from importlib_resources import as_file, files
+except ImportError:
+    from importlib.resources import as_file, files  # type: ignore
+
+try:  # Prefer stdlib so Sphinx can link to authoritative documentation
+    from importlib.resources.abc import Traversable
+except ImportError:
+    from importlib_resources.abc import Traversable
+
+__all__ = ["load"]
+
+
+class Loader:
+    """A loader for package files relative to a module
+
+    This class wraps :mod:`importlib.resources` to provide a getter
+    function with an interpreter-lifetime scope. For typical packages
+    it simply passes through filesystem paths as :class:`~pathlib.Path`
+    objects. For zipped distributions, it will unpack the files into
+    a temporary directory that is cleaned up on interpreter exit.
+
+    This loader accepts a fully-qualified module name or a module
+    object.
+
+    Expected usage::
+
+        '''Data package
+
+        .. autofunction:: load_data
+
+        .. automethod:: load_data.readable
+
+        .. automethod:: load_data.as_path
+
+        .. automethod:: load_data.cached
+        '''
+
+        from sdcflows.data import Loader
+
+        load_data = Loader(__package__)
+
+    :class:`~Loader` objects implement the :func:`callable` interface
+    and generate a docstring, and are intended to be treated and documented
+    as functions.
+
+    For greater flexibility and improved readability over the ``importlib.resources``
+    interface, explicit methods are provided to access resources.
+
+    +---------------+----------------+------------------+
+    | On-filesystem | Lifetime       | Method           |
+    +---------------+----------------+------------------+
+    | `True`        | Interpreter    | :meth:`cached`   |
+    +---------------+----------------+------------------+
+    | `True`        | `with` context | :meth:`as_path`  |
+    +---------------+----------------+------------------+
+    | `False`       | n/a            | :meth:`readable` |
+    +---------------+----------------+------------------+
+
+    It is also possible to use ``Loader`` directly::
+
+        from sdcflows.data import Loader
+
+        Loader(other_package).readable('data/resource.ext').read_text()
+
+        with Loader(other_package).as_path('data') as pkgdata:
+            # Call function that requires full Path implementation
+            func(pkgdata)
+
+        # contrast to
+
+        from importlib_resources import files, as_file
+
+        files(other_package).joinpath('data/resource.ext').read_text()
+
+        with as_file(files(other_package) / 'data') as pkgdata:
+            func(pkgdata)
+
+    .. automethod:: readable
+
+    .. automethod:: as_path
+
+    .. automethod:: cached
+    """
+
+    def __init__(self, anchor: Union[str, ModuleType]):
+        self._anchor = anchor
+        self.files = files(anchor)
+        self.exit_stack = ExitStack()
+        atexit.register(self.exit_stack.close)
+        # Allow class to have a different docstring from instances
+        self.__doc__ = self._doc
+
+    @cached_property
+    def _doc(self):
+        """Construct docstring for instances
+
+        Lists the public top-level paths inside the location, where
+        non-public means has a `.` or `_` prefix or is a 'tests'
+        directory.
+        """
+        top_level = sorted(
+            os.path.relpath(p, self.files) + "/"[: p.is_dir()]
+            for p in self.files.iterdir()
+            if p.name[0] not in (".", "_") and p.name != "tests"
+        )
+        doclines = [
+            f"Load package files relative to ``{self._anchor}``.",
+            "",
+            "This package contains the following (top-level) files/directories:",
+            "",
+            *(f"* ``{path}``" for path in top_level),
+        ]
+
+        return "\n".join(doclines)
+
+    def readable(self, *segments) -> Traversable:
+        """Provide read access to a resource through a Path-like interface.
+
+        This file may or may not exist on the filesystem, and may be
+        efficiently used for read operations, including directory traversal.
+
+        This result is not cached or copied to the filesystem in cases where
+        that would be necessary.
+        """
+        return self.files.joinpath(*segments)
+
+    def as_path(self, *segments) -> AbstractContextManager[Path]:
+        """Ensure data is available as a :class:`~pathlib.Path`.
+
+        This method generates a context manager that yields a Path when
+        entered.
+
+        This result is not cached, and any temporary files that are created
+        are deleted when the context is exited.
+        """
+        return as_file(self.files.joinpath(*segments))
+
+    @cache
+    def cached(self, *segments) -> Path:
+        """Ensure data is available as a :class:`~pathlib.Path`.
+
+        Any temporary files that are created remain available throughout
+        the duration of the program, and are deleted when Python exits.
+
+        Results are cached so that multiple calls do not unpack the same
+        data multiple times, but the cache is sensitive to the specific
+        argument(s) passed.
+        """
+        return self.exit_stack.enter_context(as_file(self.files.joinpath(*segments)))
+
+    __call__ = cached
+
+
+load = Loader(__package__)

{sdcflows-2.5.2 → sdcflows-2.6.0}/sdcflows/data/fmap-any_registration.json

@@ -18,5 +18,6 @@
     "transforms": [ "Rigid", "Rigid" ],
     "use_histogram_matching": [ true, true ],
     "winsorize_lower_quantile": 0.001,
-    "winsorize_upper_quantile": 0.999
+    "winsorize_upper_quantile": 0.999,
+    "write_composite_transform": false
 }

{sdcflows-2.5.2 → sdcflows-2.6.0}/sdcflows/data/fmap-any_registration_testing.json

@@ -18,5 +18,6 @@
     "transforms": [ "Rigid", "Rigid" ],
     "use_histogram_matching": [ true, true ],
     "winsorize_lower_quantile": 0.005,
-    "winsorize_upper_quantile": 0.998
+    "winsorize_upper_quantile": 0.998,
+    "write_composite_transform": false
 }

{sdcflows-2.5.2 → sdcflows-2.6.0}/sdcflows/fieldmaps.py

@@ -450,10 +450,10 @@ class FieldmapEstimation:
             kwargs["mode"] = str(self.method).rpartition(".")[-1].lower()
             self._wf = init_fmap_wf(**kwargs)
             self._wf.inputs.inputnode.magnitude = [
-                str(f.path) for f in self.sources if f.suffix.startswith("magnitude")
+                str(f.path.absolute()) for f in self.sources if f.suffix.startswith("magnitude")
             ]
             self._wf.inputs.inputnode.fieldmap = [
-                (str(f.path), f.metadata)
+                (str(f.path.absolute()), f.metadata)
                 for f in self.sources
                 if f.suffix in ("fieldmap", "phasediff", "phase2", "phase1")
             ]