From b24bb0737434dea1b4a36474c906c1e20fb9240e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Fri, 13 Dec 2024 19:41:03 -0500 Subject: [PATCH] STYLE: Rename tool to `NiFreeze` Rename the tool to `NiFreeze` following the voting and the discussion. --- .dockerignore | 4 +-- .gitignore | 4 +-- CONTRIBUTING.md | 4 +-- README.rst | 24 ++++++++--------- docs/developers.rst | 34 ++++++++++++------------- docs/installation.rst | 10 ++++---- docs/notebooks/dmri_covariance.ipynb | 6 ++--- docs/notebooks/dwi_gp_estimation.ipynb | 6 ++--- docs/usage.rst | 18 ++++++------- pyproject.toml | 24 ++++++++--------- src/eddymotion/__init__.py | 10 ++++---- src/eddymotion/__main__.py | 2 +- src/eddymotion/cli/run.py | 8 +++--- src/eddymotion/conftest.py | 2 +- src/eddymotion/data/splitting.py | 2 +- src/eddymotion/estimator.py | 16 ++++++------ src/eddymotion/math/tests/test_utils.py | 2 +- src/eddymotion/model/__init__.py | 6 ++--- src/eddymotion/model/_dipy.py | 4 +-- src/eddymotion/model/base.py | 6 ++--- src/eddymotion/model/dmri.py | 12 ++++----- src/eddymotion/model/gpr.py | 2 +- src/eddymotion/model/pet.py | 4 +-- src/eddymotion/registration/ants.py | 6 ++--- 24 files changed, 107 insertions(+), 109 deletions(-) diff --git a/.dockerignore b/.dockerignore index c1e659c5..4900fc10 100644 --- a/.dockerignore +++ b/.dockerignore @@ -8,8 +8,8 @@ build/**/* build dist/**/* dist -src/eddymotion.egg-info/**/* -src/eddymotion.egg-info +src/nifreeze.egg-info/**/* +src/nifreeze.egg-info .eggs/**/* .eggs diff --git a/.gitignore b/.gitignore index f14da924..ccb87f19 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,5 @@ # setuptools-scm -eddymotion/_version.py +nifreeze/_version.py # Byte-compiled / optimized / DLL files __pycache__/ @@ -115,4 +115,4 @@ ENV/ kubernetes/jobs/ # Version files -src/eddymotion/_version.py \ No newline at end of file +src/nifreeze/_version.py diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 971bdc8e..08f20ef8 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,3 +1,3 @@ -# Contributing to *eddymotion* +# Contributing to *NiFreeze* -*eddymotion* is a project of the [*NiPreps* Community, which specifies the contributing guidelines](https://www.nipreps.org/community/). \ No newline at end of file +*NiFreeze* is a project of the [*NiPreps* Community, which specifies the contributing guidelines](https://www.nipreps.org/community/). diff --git a/README.rst b/README.rst index 56aad44c..d5a39cdf 100644 --- a/README.rst +++ b/README.rst @@ -1,5 +1,5 @@ -*Eddymotion* -============ +*NiFreeze* +========== Estimating head-motion and deformations derived from eddy-currents in diffusion MRI data. .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4680599.svg @@ -7,23 +7,23 @@ Estimating head-motion and deformations derived from eddy-currents in diffusion :alt: DOI .. image:: https://img.shields.io/badge/License-Apache_2.0-blue.svg - :target: https://github.com/nipreps/eddymotion/blob/main/LICENSE + :target: https://github.com/nipreps/nifreeze/blob/main/LICENSE :alt: License -.. image:: https://img.shields.io/pypi/v/eddymotion.svg - :target: https://pypi.python.org/pypi/eddymotion/ +.. image:: https://img.shields.io/pypi/v/nifreeze.svg + :target: https://pypi.python.org/pypi/nifreeze/ :alt: Latest Version -.. image:: https://github.com/nipreps/eddymotion/actions/workflows/test.yml/badge.svg - :target: https://github.com/nipreps/eddymotion/actions/workflows/test.yml +.. image:: https://github.com/nipreps/nifreeze/actions/workflows/test.yml/badge.svg + :target: https://github.com/nipreps/nifreeze/actions/workflows/test.yml :alt: Testing -.. image:: https://github.com/nipreps/eddymotion/actions/workflows/pages/pages-build-deployment/badge.svg - :target: https://www.nipreps.org/eddymotion/main/index.html +.. image:: https://github.com/nipreps/nifreeze/actions/workflows/pages/pages-build-deployment/badge.svg + :target: https://www.nipreps.org/nifreeze/main/index.html :alt: Documentation -.. image:: https://github.com/nipreps/eddymotion/actions/workflows/pythonpackage.yml/badge.svg - :target: https://github.com/nipreps/eddymotion/actions/workflows/pythonpackage.yml +.. image:: https://github.com/nipreps/nifreeze/actions/workflows/pythonpackage.yml/badge.svg + :target: https://github.com/nipreps/nifreeze/actions/workflows/pythonpackage.yml :alt: Python package Retrospective estimation of head-motion between diffusion-weighted images (DWI) acquired within @@ -43,7 +43,7 @@ More recently, Cieslak et al. [#r3]_ integrated both approaches in *SHORELine*, (i) setting up a leave-one-out prediction framework as in eddy; and (ii) replacing eddy’s general-purpose Gaussian process prediction with the SHORE [#r4]_ diffusion model. -*Eddymotion* is an open implementation of eddy-current and head-motion correction that builds upon +*NiFreeze* is an open implementation of eddy-current and head-motion correction that builds upon the work of ``eddy`` and *SHORELine*, while generalizing these methods to multiple acquisition schemes (single-shell, multi-shell, and diffusion spectrum imaging) using diffusion models available with DIPY [#r5]_. diff --git a/docs/developers.rst b/docs/developers.rst index 400cbf53..4c5f14a1 100644 --- a/docs/developers.rst +++ b/docs/developers.rst @@ -2,23 +2,23 @@ For developers ============== Contributing ------------ -*Eddymotion* is a project of the *NiPreps Community*, `which specifies the contributing guidelines `__. +*NiFreeze* is a project of the *NiPreps Community*, `which specifies the contributing guidelines `__. Before delving into the code, please make sure you have read all the guidelines offered online. Documentation ------------- -Documentation sources are found under the ``docs/`` folder, and builds are archived in the `gh-pages `__ branch of the repository. -With GitHub Pages, the documentation is posted under https://www.nipreps.org/eddymotion. +Documentation sources are found under the ``docs/`` folder, and builds are archived in the `gh-pages `__ branch of the repository. +With GitHub Pages, the documentation is posted under https://www.nipreps.org/nifreeze. We maintain versioned documentation, by storing git tags under ``./`` folders, i.e., we do not archive every patch release, but only every minor release. In other words, folder ``0.1/`` of the documentation tree contains the documents for the latest release within the *0.1.x* series. With every commit (or merge commit) to ``main``, the *development* version of the documentation under the folder ``main/`` is updated too. -The ``gh-pages`` branch is automatically maintained with `a GitHub Action `__. +The ``gh-pages`` branch is automatically maintained with `a GitHub Action `__. Please, do not commit manually to ``gh-pages``. To build the documentation locally, you first need to make sure that ``setuptools_scm[toml] >= 6.2`` is installed in your environment and then:: - $ cd / - $ python -m setuptools_scm # This will generate ``src/eddymotion/_version.py`` + $ cd / + $ python -m setuptools_scm # This will generate ``src/nifreeze/_version.py`` $ make -C docs/ html Library API (application program interface) @@ -28,14 +28,14 @@ Information on specific functions, classes, and methods. .. toctree:: :glob: - api/eddymotion.cli - api/eddymotion.data - api/eddymotion.data.dmri - api/eddymotion.estimator - api/eddymotion.exceptions - api/eddymotion.math - api/eddymotion.model - api/eddymotion.registration - api/eddymotion.testing - api/eddymotion.utils - api/eddymotion.viz + api/nifreeze.cli + api/nifreeze.data + api/nifreeze.data.dmri + api/nifreeze.estimator + api/nifreeze.exceptions + api/nifreeze.math + api/nifreeze.model + api/nifreeze.registration + api/nifreeze.testing + api/nifreeze.utils + api/nifreeze.viz diff --git a/docs/installation.rst b/docs/installation.rst index 86e5bf8c..77f38588 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -3,18 +3,18 @@ Installation ============ -Make sure all of *eddymotion*' `External Dependencies`_ are installed. +Make sure all of *NiFreeze*' `External Dependencies`_ are installed. On a functional Python 3.7 (or above) environment with ``pip`` installed, -*eddymotion* can be installed using the habitual command :: +*NiFreeze* can be installed using the habitual command :: - $ python -m pip install eddymotion + $ python -m pip install nifreeze Check your installation with the following command line :: - $ python -c "from eddymotion import __version__; print(__version__)" + $ python -c "from nifreeze import __version__; print(__version__)" External Dependencies --------------------- -*eddymotion* requires DIPY_, and ANTs_. +*NiFreeze* requires DIPY_, and ANTs_. diff --git a/docs/notebooks/dmri_covariance.ipynb b/docs/notebooks/dmri_covariance.ipynb index e27ceff8..20c99b89 100644 --- a/docs/notebooks/dmri_covariance.ipynb +++ b/docs/notebooks/dmri_covariance.ipynb @@ -24,7 +24,7 @@ "import matplotlib.pyplot as plt\n", "import numpy as np\n", "\n", - "from eddymotion.model.gpr import (\n", + "from nifreeze.model.gpr import (\n", " compute_pairwise_angles,\n", " exponential_covariance,\n", " spherical_covariance,\n", @@ -229,7 +229,7 @@ "metadata": {}, "outputs": [], "source": [ - "from eddymotion.testing.simulations import simulate_voxels\n", + "from nifreeze.testing.simulations import simulate_voxels\n", "\n", "NUM_VOXELS = 3000\n", "BVAL_SHELL = 3000\n", @@ -345,7 +345,7 @@ } ], "source": [ - "from eddymotion.model.gpr import EddyMotionGPR, SphericalKriging\n", + "from nifreeze.model.gpr import EddyMotionGPR, SphericalKriging\n", "\n", "K = SphericalKriging(beta_a=PARAMETER_SPHERICAL_a, beta_l=PARAMETER_lambda)(X_real)\n", "K -= K.min()\n", diff --git a/docs/notebooks/dwi_gp_estimation.ipynb b/docs/notebooks/dwi_gp_estimation.ipynb index 4ef57d3a..a9b3a479 100644 --- a/docs/notebooks/dwi_gp_estimation.ipynb +++ b/docs/notebooks/dwi_gp_estimation.ipynb @@ -4,9 +4,7 @@ "cell_type": "markdown", "id": "d11e5969ed6af8a5", "metadata": {}, - "source": [ - "Estimate a DWI signal using the eddymotion Gaussian Process (GP) regressor estimator." - ] + "source": "Estimate a DWI signal using the nifreeze Gaussian Process (GP) regressor estimator." }, { "cell_type": "markdown", @@ -143,7 +141,7 @@ "metadata": {}, "outputs": [], "source": [ - "from eddymotion.model.gpr import EddyMotionGPR, SphericalKriging\n", + "from nifreeze.model.gpr import EddyMotionGPR, SphericalKriging\n", "\n", "beta_a = 1.38\n", "beta_l = 1 / 2.1\n", diff --git a/docs/usage.rst b/docs/usage.rst index a02fbe9f..e6cfa816 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -2,17 +2,17 @@ How to Use ========== -Incorporating Eddymotion into a Python module or script -------------------------------------------------------- -To utilize Eddymotion functionalities within your Python module or script, follow these steps: +Incorporating NiFreeze into a Python module or script +----------------------------------------------------- +To utilize NiFreeze functionalities within your Python module or script, follow these steps: -1. **Import Eddymotion Components**: Start by importing necessary components from the Eddymotion package: +1. **Import NiFreeze Components**: Start by importing necessary components from the NiFreeze package: .. code-block:: python - # Import required components from the Eddymotion package - from eddymotion.data import dmri - from eddymotion.estimator import EddyMotionEstimator + # Import required components from the NiFreeze package + from nifreeze.data import dmri + from nifreeze.estimator import EddyMotionEstimator 2. **Load DWI Data**: Load diffusion MRI (dMRI) data into a `DWI` object using the `load` function. Ensure the gradient table is provided. It should have one row per diffusion-weighted image. The first three columns represent the gradient directions, and the last column indicates the timing and strength of the gradients in units of s/mm² [ R A S+ b ]. If your data are in NIfTI file format, include a file containing the gradient information with the argument "gradients_file": @@ -32,7 +32,7 @@ To utilize Eddymotion functionalities within your Python module or script, follo dwi_data = dmri.DWI.from_filename('/path/to/downloaded/dwi_full.h5') -3. **Instantiate an Eddymotion Estimator Object**: Create an instance of the `EddyMotionEstimator` class, which encapsulates tools for estimating rigid-body head motion and distortions due to eddy currents. +3. **Instantiate an NiFreeze Estimator Object**: Create an instance of the `EddyMotionEstimator` class, which encapsulates tools for estimating rigid-body head motion and distortions due to eddy currents. .. code-block:: python @@ -59,7 +59,7 @@ To utilize Eddymotion functionalities within your Python module or script, follo - `dwi_data`: The target DWI dataset, represented by this tool's internal type. - `align_kwargs`: Parameters to configure the image registration process. - - `models`: list of diffusion models used to generate the registration target for each gradient map. For a list of available models, see :doc:`api/eddymotion.model`. + - `models`: list of diffusion models used to generate the registration target for each gradient map. For a list of available models, see :doc:`api/nifreeze.model`. - `omp_nthreads`: Maximum number of threads an individual process may use. - `n_jobs`: Number of parallel jobs. - `seed`: Seed for the random number generator (necessary for deterministic estimation). diff --git a/pyproject.toml b/pyproject.toml index 8bed5680..68df1e9a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "hatchling.build" [project] -name = "eddymotion" +name = "nifreeze" description = "Pure python eddy-current and head-motion correction for dMRI, an extension of QSIprep's SHOREline algorithm (Cieslak, 2020) to multiple diffusion models." readme = "README.rst" authors = [{name = "The NiPreps Developers", email = "nipreps@gmail.com"}] @@ -34,8 +34,8 @@ dependencies = [ dynamic = ["version"] [project.urls] -Documentation = "https://www.nipreps.org/eddymotion" -Home = "https://github.com/nipreps/eddymotion" +Documentation = "https://www.nipreps.org/nifreeze" +Home = "https://github.com/nipreps/nifreeze" NiPreps = "https://www.nipreps.org/" [project.optional-dependencies] @@ -80,12 +80,12 @@ antsopt = [ ] # Aliases -docs = ["eddymotion[doc]"] -tests = ["eddymotion[test]"] -all = ["eddymotion[doc,test,dev,plotting,resmon,antsopt]"] +docs = ["nifreeze[doc]"] +tests = ["nifreeze[test]"] +all = ["nifreeze[doc,test,dev,plotting,resmon,antsopt]"] [project.scripts] -eddymotion = "eddymotion.cli.run:main" +nifreeze = "nifreeze.cli.run:main" # # Hatch configurations @@ -98,9 +98,9 @@ allow-direct-references = true exclude = [".git_archival.txt"] # No longer needed in sdist [tool.hatch.build.targets.wheel] -packages = ["src/eddymotion"] +packages = ["src/nifreeze"] # exclude = [ -# "eddymotion/tests/data", # Large test data directory +# "nifreeze/tests/data", # Large test data directory # ] @@ -114,7 +114,7 @@ local_scheme = "no-local-version" [tool.hatch.build.hooks.vcs] -version-file = "src/eddymotion/_version.py" +version-file = "src/nifreeze/_version.py" # # Developer tool configurations @@ -161,7 +161,7 @@ inline-quotes = "double" quote-style = "double" [tool.ruff.lint.isort] -known-first-party=["eddymotion"] +known-first-party=["nifreeze"] [tool.pytest.ini_options] pythonpath = "src/ test/" @@ -181,7 +181,7 @@ omit = [ '*/viz/*', '*/__init__.py', '*/conftest.py', - 'src/eddymotion/_version.py' + 'src/nifreeze/_version.py' ] [tool.coverage.report] diff --git a/src/eddymotion/__init__.py b/src/eddymotion/__init__.py index 412aab1f..44357f70 100644 --- a/src/eddymotion/__init__.py +++ b/src/eddymotion/__init__.py @@ -20,12 +20,12 @@ # # https://www.nipreps.org/community/licensing/ # -"""Top-level package for eddymotion.""" +"""Top-level package for NiFreeze.""" -from eddymotion._version import __version__ +from nifreeze._version import __version__ -__packagename__ = "eddymotion" -__copyright__ = "Copyright 2021, The eddymotion developers" -__url__ = "https://github.com/nipreps/EddyMotionCorrection" +__packagename__ = "nifreeze" +__copyright__ = "Copyright 2021, The NiPreps developers" +__url__ = "https://github.com/nipreps/nifreeze" DOWNLOAD_URL = f"https://github.com/nipreps/{__packagename__}/archive/{__version__}.tar.gz" diff --git a/src/eddymotion/__main__.py b/src/eddymotion/__main__.py index 183d1dad..80f8b87d 100644 --- a/src/eddymotion/__main__.py +++ b/src/eddymotion/__main__.py @@ -20,7 +20,7 @@ # # https://www.nipreps.org/community/licensing/ # -"""Entry point for Eddymotion.""" +"""Entry point for NiFreeze.""" import sys diff --git a/src/eddymotion/cli/run.py b/src/eddymotion/cli/run.py index b68e83b7..86bb83d3 100644 --- a/src/eddymotion/cli/run.py +++ b/src/eddymotion/cli/run.py @@ -20,13 +20,13 @@ # # https://www.nipreps.org/community/licensing/ # -"""Eddymotion runner.""" +"""NiFreeze runner.""" from pathlib import Path -from eddymotion.cli.parser import parse_args -from eddymotion.data.dmri import DWI -from eddymotion.estimator import EddyMotionEstimator +from nifreeze.cli.parser import parse_args +from nifreeze.data.dmri import DWI +from nifreeze.estimator import EddyMotionEstimator def main(argv=None) -> None: diff --git a/src/eddymotion/conftest.py b/src/eddymotion/conftest.py index a867fef7..f9a4cfa4 100644 --- a/src/eddymotion/conftest.py +++ b/src/eddymotion/conftest.py @@ -29,7 +29,7 @@ import numpy import pytest -test_data_env = os.getenv("TEST_DATA_HOME", str(Path.home() / "eddymotion-tests")) +test_data_env = os.getenv("TEST_DATA_HOME", str(Path.home() / "nifreeze-tests")) test_output_dir = os.getenv("TEST_OUTPUT_DIR") test_workdir = os.getenv("TEST_WORK_DIR") diff --git a/src/eddymotion/data/splitting.py b/src/eddymotion/data/splitting.py index 66c03699..fca0f7b9 100644 --- a/src/eddymotion/data/splitting.py +++ b/src/eddymotion/data/splitting.py @@ -34,7 +34,7 @@ def lovo_split(dataset, index, with_b0=False): Parameters ---------- - dataset : :obj:`eddymotion.data.dmri.DWI` + dataset : :obj:`nifreeze.data.dmri.DWI` DWI object index : :obj:`int` Index of the DWI orientation to be left out in this fold. diff --git a/src/eddymotion/estimator.py b/src/eddymotion/estimator.py index ada6bccb..3ee9122b 100644 --- a/src/eddymotion/estimator.py +++ b/src/eddymotion/estimator.py @@ -28,10 +28,10 @@ import nibabel as nb from tqdm import tqdm -from eddymotion import utils as eutils -from eddymotion.data.splitting import lovo_split -from eddymotion.model.base import ModelFactory -from eddymotion.registration.ants import _prepare_registration_data, _run_registration +from nifreeze import utils as eutils +from nifreeze.data.splitting import lovo_split +from nifreeze.model.base import ModelFactory +from nifreeze.registration.ants import _prepare_registration_data, _run_registration class EddyMotionEstimator: @@ -53,7 +53,7 @@ def estimate( Parameters ---------- - dwdata : :obj:`~eddymotion.dmri.DWI` + dwdata : :obj:`~nifreeze.dmri.DWI` The target DWI dataset, represented by this tool's internal type. The object is used in-place, and will contain the estimated parameters in its ``em_affines`` property, as well as the rotated @@ -67,7 +67,7 @@ def estimate( models : :obj:`list` Selects the diffusion model that will generate the registration target corresponding to each gradient map. - See :obj:`~eddymotion.model.ModelFactory` for allowed models (and corresponding + See :obj:`~nifreeze.model.ModelFactory` for allowed models (and corresponding keywords). omp_nthreads : :obj:`int` Maximum number of threads an individual process may use. @@ -228,12 +228,12 @@ def _prepare_kwargs(dwdata, kwargs): Parameters ---------- - dwdata : :class:`eddymotion.data.dmri.DWI` + dwdata : :class:`nifreeze.data.dmri.DWI` DWI data object. kwargs : :obj:`dict` Keyword arguments. """ - from eddymotion.data.filtering import advanced_clip as _advanced_clip + from nifreeze.data.filtering import advanced_clip as _advanced_clip if dwdata.brainmask is not None: kwargs["mask"] = dwdata.brainmask diff --git a/src/eddymotion/math/tests/test_utils.py b/src/eddymotion/math/tests/test_utils.py index 49702332..84618100 100644 --- a/src/eddymotion/math/tests/test_utils.py +++ b/src/eddymotion/math/tests/test_utils.py @@ -23,7 +23,7 @@ import numpy as np import pytest -from eddymotion.math.utils import compute_angle, is_positive_definite +from nifreeze.math.utils import compute_angle, is_positive_definite def test_is_positive_definite(): diff --git a/src/eddymotion/model/__init__.py b/src/eddymotion/model/__init__.py index 149a71ec..886b698b 100644 --- a/src/eddymotion/model/__init__.py +++ b/src/eddymotion/model/__init__.py @@ -22,18 +22,18 @@ # """Data models.""" -from eddymotion.model.base import ( +from nifreeze.model.base import ( AverageModel, ModelFactory, TrivialModel, ) -from eddymotion.model.dmri import ( +from nifreeze.model.dmri import ( AverageDWModel, DKIModel, DTIModel, GPModel, ) -from eddymotion.model.pet import PETModel +from nifreeze.model.pet import PETModel __all__ = ( "ModelFactory", diff --git a/src/eddymotion/model/_dipy.py b/src/eddymotion/model/_dipy.py index d7eb1773..5025421c 100644 --- a/src/eddymotion/model/_dipy.py +++ b/src/eddymotion/model/_dipy.py @@ -31,7 +31,7 @@ from dipy.reconst.base import ReconstModel from sklearn.gaussian_process import GaussianProcessRegressor -from eddymotion.model.gpr import ( +from nifreeze.model.gpr import ( EddyMotionGPR, ExponentialKriging, SphericalKriging, @@ -157,7 +157,7 @@ def fit( Returns ------- - :obj:`~eddymotion.model.dipy.GPFit` + :obj:`~nifreeze.model.dipy.GPFit` A model fit container object. """ diff --git a/src/eddymotion/model/base.py b/src/eddymotion/model/base.py index 1bf8f01b..17591647 100644 --- a/src/eddymotion/model/base.py +++ b/src/eddymotion/model/base.py @@ -20,11 +20,11 @@ # # https://www.nipreps.org/community/licensing/ # -"""Base infrastructure for eddymotion's models.""" +"""Base infrastructure for nifreeze's models.""" import numpy as np -from eddymotion.exceptions import ModelNotFittedError +from nifreeze.exceptions import ModelNotFittedError class ModelFactory: @@ -51,7 +51,7 @@ def init(model="DTI", **kwargs): return TrivialModel(predicted=kwargs.pop("S0"), gtab=kwargs.pop("gtab")) if model.lower() in ("avgdwi", "averagedwi", "meandwi"): - from eddymotion.model.dmri import AverageDWModel + from nifreeze.model.dmri import AverageDWModel return AverageDWModel(**kwargs) diff --git a/src/eddymotion/model/dmri.py b/src/eddymotion/model/dmri.py index 6241fab1..82e59934 100644 --- a/src/eddymotion/model/dmri.py +++ b/src/eddymotion/model/dmri.py @@ -24,9 +24,9 @@ import numpy as np from joblib import Parallel, delayed -from eddymotion.exceptions import ModelNotFittedError -from eddymotion.model._dipy import _rasb2dipy -from eddymotion.model.base import BaseModel +from nifreeze.exceptions import ModelNotFittedError +from nifreeze.model._dipy import _rasb2dipy +from nifreeze.model.base import BaseModel def _exec_fit(model, data, chunk=None): @@ -238,7 +238,7 @@ def __init__(self, **kwargs): bias : :obj:`bool` Whether the overall distribution of each diffusion weighted image will be standardized and centered around the - :data:`src.eddymotion.model.base.DEFAULT_CLIP_PERCENTILE` percentile. + :data:`src.nifreeze.model.base.DEFAULT_CLIP_PERCENTILE` percentile. stat : :obj:`str` Whether the summary statistic to apply is ``"mean"`` or ``"median"``. @@ -310,10 +310,10 @@ class DKIModel(BaseDWIModel): class GPModel(BaseDWIModel): - """A wrapper of :obj:`~eddymotion.model.dipy.GaussianProcessModel`.""" + """A wrapper of :obj:`~nifreeze.model.dipy.GaussianProcessModel`.""" _modelargs = ("kernel_model",) - _model_class = "eddymotion.model._dipy.GaussianProcessModel" + _model_class = "nifreeze.model._dipy.GaussianProcessModel" def find_shelling_scheme( diff --git a/src/eddymotion/model/gpr.py b/src/eddymotion/model/gpr.py index 1d1c4da6..6f739156 100644 --- a/src/eddymotion/model/gpr.py +++ b/src/eddymotion/model/gpr.py @@ -64,7 +64,7 @@ class EddyMotionGPR(GaussianProcessRegressor): r""" - A GP regressor specialized for eddymotion. + A GP regressor specialized for nifreeze. This specialization of the default GP regressor is created to allow the following extended behaviors: diff --git a/src/eddymotion/model/pet.py b/src/eddymotion/model/pet.py index f6e1299c..1773367e 100644 --- a/src/eddymotion/model/pet.py +++ b/src/eddymotion/model/pet.py @@ -25,8 +25,8 @@ import numpy as np from joblib import Parallel, delayed -from eddymotion.exceptions import ModelNotFittedError -from eddymotion.model.base import BaseModel +from nifreeze.exceptions import ModelNotFittedError +from nifreeze.model.base import BaseModel DEFAULT_TIMEFRAME_MIDPOINT_TOL = 1e-2 """Time frame tolerance in seconds.""" diff --git a/src/eddymotion/registration/ants.py b/src/eddymotion/registration/ants.py index 2f1c9495..f01978d2 100644 --- a/src/eddymotion/registration/ants.py +++ b/src/eddymotion/registration/ants.py @@ -78,7 +78,7 @@ def _to_nifti( """ data = np.squeeze(data) if clip: - from eddymotion.data.filtering import advanced_clip + from nifreeze.data.filtering import advanced_clip data = advanced_clip(data) nii = nb.Nifti1Image( @@ -162,7 +162,7 @@ def _get_ants_settings(settings: str = "b0-to-b0_level0") -> Path: """ return Path( pkg_fn( - "eddymotion.registration", + "nifreeze.registration", f"config/{settings}.json", ) ) @@ -461,7 +461,7 @@ def _run_registration( registration = Registration( terminal_output="file", from_file=pkg_fn( - "eddymotion.registration", + "nifreeze.registration", f"config/{reg_target_type[0]}-to-{reg_target_type[1]}_level{i_iter}.json", ), fixed_image=str(fixed.absolute()),