maint: address some remaining "eddymotion" mentions

Author: nipreps-bot

.github/workflows/contrib.yml

@@ -19,7 +19,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3
-      - name: Lint EddyMotion
+      - name: Lint NiFreeze
         run: pipx run ruff check --diff
-      - name: Format EddyMotion
+      - name: Format NiFreeze
         run: pipx run ruff format --diff

docs/conf.py

@@ -175,8 +175,8 @@
 latex_documents = [
     (
         master_doc,
-        "smriprep.tex",
-        "Eddymotion Documentation",
+        "nifreeze.tex",
+        "NiFreeze Documentation",
         "The NiPreps Developers",
         "manual",
     ),
@@ -187,7 +187,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "smriprep", "Eddymotion Documentation", [author], 1)]
+man_pages = [(master_doc, "nifreeze", "NiFreeze Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -198,10 +198,10 @@
 texinfo_documents = [
     (
         master_doc,
-        "smriprep",
-        "Eddymotion Documentation",
+        "nifreeze",
+        "NiFreeze Documentation",
         author,
-        "Eddymotion",
+        "NiFreeze",
         "One line description of project.",
         "Miscellaneous",
     ),

docs/developers.rst

@@ -2,7 +2,7 @@ For developers
 ==============
 Contributing
 ------------
-*Eddymotion* is a project of the *NiPreps Community*, `which specifies the contributing guidelines <https://www.nipreps.org/community/>`__.
+*NiFreeze* is a project of the *NiPreps Community*, `which specifies the contributing guidelines <https://www.nipreps.org/community/>`__.
 Before delving into the code, please make sure you have read all the guidelines offered online.
 
 Documentation

docs/notebooks/dmri_covariance.ipynb

@@ -345,7 +345,7 @@
     }
    ],
    "source": [
-    "from nifreeze.model.gpr import EddyMotionGPR, SphericalKriging\n",
+    "from nifreeze.model.gpr import DiffusionGPR, SphericalKriging\n",
     "\n",
     "K = SphericalKriging(beta_a=PARAMETER_SPHERICAL_a, beta_l=PARAMETER_lambda)(X_real)\n",
     "K -= K.min()\n",
@@ -382,7 +382,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "gpm = EddyMotionGPR(\n",
+    "gpm = DiffusionGPR(\n",
     "    kernel=SphericalKriging(beta_a=PARAMETER_SPHERICAL_a, beta_l=PARAMETER_lambda),\n",
     "    alpha=0.1,\n",
     "    disp=True,\n",

docs/notebooks/dwi_gp_estimation.ipynb

@@ -133,7 +133,7 @@
    "id": "9dcab811fe667617",
    "metadata": {},
    "source": [
-    "Define the EddyMotionGPR instance."
+    "Define the DiffusionGPR instance."
    ]
   },
   {
@@ -143,7 +143,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from nifreeze.model.gpr import EddyMotionGPR, SphericalKriging\n",
+    "from nifreeze.model.gpr import DiffusionGPR, SphericalKriging\n",
     "\n",
     "beta_a = 1.38\n",
     "beta_l = 1 / 2.1\n",
@@ -152,7 +152,7 @@
     "alpha = 0.1\n",
     "disp = True\n",
     "optimizer = None\n",
-    "gpr = EddyMotionGPR(kernel=kernel, alpha=alpha, disp=disp, optimizer=optimizer)"
+    "gpr = DiffusionGPR(kernel=kernel, alpha=alpha, disp=disp, optimizer=optimizer)"
    ]
   },
   {
@@ -302,7 +302,7 @@
     }
    ],
    "source": [
-    "gpr = EddyMotionGPR(kernel=kernel, alpha=alpha, disp=disp, optimizer=\"fmin_l_bfgs_b\", ftol=0.1)\n",
+    "gpr = DiffusionGPR(kernel=kernel, alpha=alpha, disp=disp, optimizer=\"fmin_l_bfgs_b\", ftol=0.1)\n",
     "gpr = gpr.fit(bvecs_shell, y.T)"
    ]
   },
@@ -351,7 +351,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "gpr = EddyMotionGPR(kernel=gpr.kernel_, alpha=alpha, disp=disp, optimizer=None)\n",
+    "gpr = DiffusionGPR(kernel=gpr.kernel_, alpha=alpha, disp=disp, optimizer=None)\n",
     "gpr = gpr.fit(X_train, y_train.T)\n",
     "y_sim2 = np.squeeze(gpr.predict(X_test))\n",
     "\n",

docs/running.rst

@@ -1,7 +1,7 @@
 .. _running_nifreeze:
 
-Running *Eddymotion*
-********************
+Running *NiFreeze*
+******************
 Command line interface
 ----------------------
 .. argparse::

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
+      # Import required components from the nifreeze package
       from nifreeze.data import dmri
-      from nifreeze.estimator import EddyMotionEstimator
+      from nifreeze.estimator import Estimator
 
 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":
 
@@ -32,16 +32,16 @@ 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 `Estimator` class, which encapsulates tools for estimating rigid-body head motion and distortions due to eddy currents.
 
    .. code-block:: python
 
-      # Create an instance of the EddyMotionEstimator class
-      estimator = EddyMotionEstimator()
+      # Create an instance of the Estimator class
+      estimator = Estimator()
 
 4. **Fit the Models to Estimate the Affine Transformation**:
 
-   Use the `estimate` method of the `EddyMotionEstimator` object to estimate the affine transformation parameters:
+   Use the `estimate` method of the `Estimator` object to estimate the affine transformation parameters:
 
    .. code-block:: python
 

scripts/dwi_gp_estimation_error_analysis.py

@@ -37,7 +37,7 @@
 from sklearn.model_selection import KFold, RepeatedKFold, cross_val_predict, cross_val_score
 
 from nifreeze.model.gpr import (
-    EddyMotionGPR,
+    DiffusionGPR,
     SphericalKriging,
 )
 from nifreeze.testing import simulations as testsims
@@ -48,7 +48,7 @@ def cross_validate(
     y: np.ndarray,
     cv: int,
     n_repeats: int,
-    gpr: EddyMotionGPR,
+    gpr: DiffusionGPR,
 ) -> dict[int, list[tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]]]:
     """
     Perform the experiment by estimating the dMRI signal using a Gaussian process model.
@@ -63,7 +63,7 @@ def cross_validate(
         Number of folds.
     n_repeats : :obj:`int`
         Number of times the cross-validator needs to be repeated.
-    gpr : obj:`~nifreeze.model.gpr.EddyMotionGPR`
+    gpr : obj:`~nifreeze.model.gpr.DiffusionGPR`
         The nifreeze Gaussian process regressor object.
 
     Returns
@@ -192,7 +192,7 @@ def main() -> None:
     a = 1.15
     lambda_s = 120
     alpha = 1
-    gpr = EddyMotionGPR(
+    gpr = DiffusionGPR(
         kernel=SphericalKriging(beta_a=a, beta_l=lambda_s),
         alpha=alpha,
         optimizer=None,

scripts/dwi_gp_estimation_simulated_signal.py

@@ -33,7 +33,7 @@
 import numpy as np
 from dipy.core.sphere import Sphere
 
-from nifreeze.model.gpr import EddyMotionGPR, SphericalKriging
+from nifreeze.model.gpr import DiffusionGPR, SphericalKriging
 from nifreeze.testing import simulations as testsims
 
 SAMPLING_DIRECTIONS = 200
@@ -135,7 +135,7 @@ def main() -> None:
     a = 1.15
     lambda_s = 120
     alpha = 100
-    gpr = EddyMotionGPR(
+    gpr = DiffusionGPR(
         kernel=SphericalKriging(a=a, lambda_s=lambda_s),
         alpha=alpha,
         optimizer=None,

src/nifreeze/__init__.py

@@ -1,7 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 #
-# Copyright 2022 The NiPreps Developers <[email protected]>
+# Copyright The NiPreps Developers <[email protected]>
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -25,7 +25,7 @@
 from nifreeze._version import __version__
 
 __packagename__ = "nifreeze"
-__copyright__ = "Copyright 2021, The nifreeze developers"
-__url__ = "https://github.com/nipreps/EddyMotionCorrection"
+__copyright__ = "Copyright 2024, The NiFreeze developers"
+__url__ = "https://github.com/nipreps/nifreeze"
 
 DOWNLOAD_URL = f"https://github.com/nipreps/{__packagename__}/archive/{__version__}.tar.gz"

src/nifreeze/__main__.py

@@ -20,7 +20,7 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
-"""Entry point for Eddymotion."""
+"""Entry point for NiFreeze."""
 
 import sys
 

src/nifreeze/cli/run.py

@@ -20,13 +20,13 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
-"""Eddymotion runner."""
+"""NiFreeze runner."""
 
 from pathlib import Path
 
 from nifreeze.cli.parser import parse_args
 from nifreeze.data.dmri import DWI
-from nifreeze.estimator import EddyMotionEstimator
+from nifreeze.estimator import Estimator
 
 
 def main(argv=None) -> None:
@@ -42,7 +42,7 @@ def main(argv=None) -> None:
     # Open the data with the given file path
     dwi_dataset: DWI = DWI.from_filename(args.input_file)
 
-    estimator: EddyMotionEstimator = EddyMotionEstimator()
+    estimator: Estimator = Estimator()
 
     _ = estimator.estimate(
         dwi_dataset,

src/nifreeze/estimator.py

@@ -34,7 +34,7 @@
 from nifreeze.registration.ants import _prepare_registration_data, _run_registration
 
 
-class EddyMotionEstimator:
+class Estimator:
     """Estimates rigid-body head-motion and distortions derived from eddy-currents."""
 
     @staticmethod

src/nifreeze/model/_dipy.py

@@ -32,7 +32,7 @@
 from sklearn.gaussian_process import GaussianProcessRegressor
 
 from nifreeze.model.gpr import (
-    EddyMotionGPR,
+    DiffusionGPR,
     ExponentialKriging,
     SphericalKriging,
 )
@@ -180,7 +180,7 @@ def fit(
                 f"and gradient table ({grad_dirs})."
             )
 
-        gpr = EddyMotionGPR(
+        gpr = DiffusionGPR(
             kernel=self.kernel,
             random_state=random_state,
             n_targets=y.shape[1],

src/nifreeze/model/gpr.py

@@ -62,7 +62,7 @@
 """A set of supported optimizers (automatically created)."""
 
 
-class EddyMotionGPR(GaussianProcessRegressor):
+class DiffusionGPR(GaussianProcessRegressor):
     r"""
     A Gaussian process (GP) regressor specialized for nifreeze.
 

test/test_integration.py

@@ -29,7 +29,7 @@
 import numpy as np
 
 from nifreeze.data.dmri import DWI
-from nifreeze.estimator import EddyMotionEstimator
+from nifreeze.estimator import Estimator
 from nifreeze.registration.utils import displacements_within_mask
 
 
@@ -70,7 +70,7 @@ def test_proximity_estimator_trivial_model(datadir, tmp_path):
         brainmask=dwdata.brainmask,
     )
 
-    estimator = EddyMotionEstimator()
+    estimator = Estimator()
     em_affines = estimator.estimate(
         data=dwi_motion,
         models=("b0",),