Merge branch 'main' into TestAbsentMaskWarning

Author: oesteban

.github/workflows/benchmark.yml

@@ -0,0 +1,59 @@
+name: Benchmark
+
+on:
+  push:
+    branches:
+      - main
+      - maint/*
+  pull_request:
+    branches:
+      - main
+      - maint/*
+  # Allow job to be triggered manually from GitHub interface
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  benchmark:
+    name: Linux
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ '3.11' ]
+
+    steps:
+    - name: Set up system
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[antsopt,benchmark]
+    - name: Set threading parameters for reliable benchmarking
+      run: |
+        export OPENBLAS_NUM_THREADS=1
+        export MKL_NUM_THREADS=1
+        export OMP_NUM_THREADS=1
+    - name: Run benchmarks
+      run: |
+        asv machine --yes --config benchmarks/asv.conf.json
+        asv run --config benchmarks/asv.conf.json --show-stderr

.github/workflows/test.yml

@@ -70,6 +70,10 @@ jobs:
         with:
           path: /home/runner/nifreeze-tests/
           key: data-v0
+      - name: Install TeX Live
+        run: |
+          sudo apt-get update
+          sudo apt install texlive texlive-latex-extra texlive-fonts-recommended cm-super dvipng
       - name: Install tox
         run: |
           python -m pip install --upgrade pip
@@ -91,8 +95,7 @@ jobs:
     continue-on-error: true
     strategy:
       matrix:
-        check: ['spellcheck']
-
+        check: ['spellcheck', 'typecheck']
     steps:
       - uses: actions/checkout@v4
       - name: Install the latest version of uv

benchmarks/README.rst

@@ -0,0 +1,41 @@
+..  -*- rst -*-
+
+===================
+NiFreeze benchmarks
+===================
+Benchmarking NiFreeze with Airspeed Velocity.
+
+Usage
+-----
+Airspeed Velocity manages building and Python environments by itself,
+unless told otherwise.
+To run the benchmarks, you do not need to install
+a development version of *NiFreeze* on your current
+*Python* environment.
+
+To run all benchmarks for the latest commit, navigate to *NiFreeze*'s root
+``benchmarks`` directory and execute::
+
+    asv run
+
+For testing benchmarks locally, it may be better to run these without
+replications::
+
+    export REGEXP="bench.*Ufunc"
+    asv run --dry-run --show-stderr --python=same --quick -b $REGEXP
+
+All of the commands above display the results in plain text in the console,
+and the results are not saved for comparison with future commits.
+For greater control, a graphical view, and to have results saved for future
+comparisons, you can run ASV as follows to record results and generate
+the HTML reports::
+
+    asv run --skip-existing-commits --steps 10 ALL
+    asv publish
+    asv preview
+
+More on how to use ``asv`` can be found in the `ASV documentation`_.
+Command-line help is available as usual via ``asv --help`` and
+``asv run --help``.
+
+.. _ASV documentation: https://asv.readthedocs.io/

benchmarks/asv.conf.json

@@ -0,0 +1,98 @@
+{
+    // The version of the config file format.  Do not change, unless
+    // you know what you are doing.
+    "version": 1,
+
+    // The name of the project being benchmarked
+    "project": "nifreeze",
+
+    // The project's homepage
+    "project_url": "https://www.nipreps.org/nifreeze/",
+
+    // The URL or local path of the source code repository for the
+    // project being benchmarked
+    "repo": "..",
+
+    // List of branches to benchmark. If not provided, defaults to "master"
+    // (for git) or "tip" (for mercurial).
+    "branches": ["HEAD"],
+
+    "build_command": [
+        "python -m build --wheel -o {build_cache_dir} {build_dir}"
+    ],
+
+    // The DVCS being used.  If not set, it will be automatically
+    // determined from "repo" by looking at the protocol in the URL
+    // (if remote), or by looking for special directories, such as
+    // ".git" (if local).
+    "dvcs": "git",
+
+    // The tool to use to create environments.  May be "conda",
+    // "virtualenv" or other value depending on the plugins in use.
+    // If missing or the empty string, the tool will be automatically
+    // determined by looking for tools on the PATH environment
+    // variable.
+    "environment_type": "virtualenv",
+
+    // the base URL to show a commit for the project.
+    "show_commit_url": "https://github.com/nipreps/nifreeze/commit/",
+
+    // The Pythons you'd like to test against.  If not provided, defaults
+    // to the current version of Python used to run `asv`.
+    // "pythons": ["3.12"],
+
+    // The matrix of dependencies to test.  Each key is the name of a
+    // package (in PyPI) and the values are version numbers.  An empty
+    // list indicates to just test against the default (latest)
+    // version.
+    "matrix": {
+        "dipy": [],
+        "nipype": [],
+        "nest-asyncio": [],
+        "nitransforms": [],
+        "numpy": [],
+        "scikit_learn": [],
+        "scipy": []
+    },
+
+    // The directory (relative to the current directory) that benchmarks are
+    // stored in.  If not provided, defaults to "benchmarks"
+    "benchmark_dir": "benchmarks",
+
+    // The directory (relative to the current directory) to cache the Python
+    // environments in.  If not provided, defaults to "env"
+    "env_dir": "env",
+
+
+    // The directory (relative to the current directory) that raw benchmark
+    // results are stored in.  If not provided, defaults to "results".
+    "results_dir": "results",
+
+    // The directory (relative to the current directory) that the html tree
+    // should be written to.  If not provided, defaults to "html".
+    "html_dir": "html",
+
+    // The number of characters to retain in the commit hashes.
+    // "hash_length": 8,
+
+    // `asv` will cache wheels of the recent builds in each
+    // environment, making them faster to install next time.  This is
+    // number of builds to keep, per environment.
+    "build_cache_size": 8,
+
+    // The commits after which the regression search in `asv publish`
+    // should start looking for regressions. Dictionary whose keys are
+    // regexps matching to benchmark names, and values corresponding to
+    // the commit (exclusive) after which to start looking for
+    // regressions.  The default is to start from the first commit
+    // with results. If the commit is `null`, regression detection is
+    // skipped for the matching benchmark.
+    //
+    // "regressions_first_commits": {
+    //    "some_benchmark": "352cdf",  // Consider regressions only after this commit
+    //    "another_benchmark": null,   // Skip regression detection altogether
+    // }
+
+    // Maximum time in seconds that a benchmark is allowed to run before it is terminated.
+    "default_benchmark_timeout": 240
+}

benchmarks/benchmarks/__init__.py

@@ -0,0 +1,102 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# 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.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Benchmarking for nifreeze's models."""
+
+from abc import ABC
+
+import dipy.data as dpd
+import nibabel as nb
+import numpy as np
+from dipy.core.gradients import get_bval_indices
+from dipy.io import read_bvals_bvecs
+from dipy.segment.mask import median_otsu
+from scipy.ndimage import binary_dilation
+from skimage.morphology import ball
+
+from nifreeze.model.gpr import DiffusionGPR, SphericalKriging
+
+
+class DiffusionGPRBenchmark(ABC):
+    def __init__(self):
+        self._estimator = None
+        self._X_train = None
+        self._y_train = None
+        self._X_test = None
+        self._y_test = None
+
+    def setup(self, *args, **kwargs):
+        beta_a = 1.38
+        beta_l = 1 / 2.1
+        alpha = 0.1
+        disp = True
+        optimizer = None
+        self.make_estimator((beta_a, beta_l, alpha, disp, optimizer))
+        self.make_data()
+
+    def make_estimator(self, params):
+        beta_a, beta_l, alpha, disp, optimizer = params
+        kernel = SphericalKriging(beta_a=beta_a, beta_l=beta_l)
+        self._estimator = DiffusionGPR(
+            kernel=kernel,
+            alpha=alpha,
+            disp=disp,
+            optimizer=optimizer,
+        )
+
+    def make_data(self):
+        name = "sherbrooke_3shell"
+
+        dwi_fname, bval_fname, bvec_fname = dpd.get_fnames(name=name)
+        dwi_data = nb.load(dwi_fname).get_fdata()
+        bvals, bvecs = read_bvals_bvecs(bval_fname, bvec_fname)
+
+        _, brain_mask = median_otsu(dwi_data, vol_idx=[0])
+        brain_mask = binary_dilation(brain_mask, ball(8))
+
+        bval = 1000
+        indices = get_bval_indices(bvals, bval, tol=20)
+
+        bvecs_shell = bvecs[indices]
+        shell_data = dwi_data[..., indices]
+        dwi_vol_idx = len(indices) // 2
+
+        # Prepare a train/test mask (False for all directions except the left-out where it's true)
+        train_test_mask = np.zeros(bvecs_shell.shape[0], dtype=bool)
+        train_test_mask[dwi_vol_idx] = True
+
+        # Generate train/test bvecs
+        self._X_train = bvecs_shell[~train_test_mask, :]
+        self._X_test = bvecs_shell[train_test_mask, :]
+
+        # Select voxels within brain mask
+        y = shell_data[brain_mask]
+
+        # Generate train/test data
+        self._y_train = y[:, ~train_test_mask]
+        self._y_test = y[:, train_test_mask]
+
+    def time_fit(self, *args):
+        self._estimator = self._estimator.fit(self._X_train, self._y_train.T)
+
+    def time_predict(self):
+        self._estimator.predict(self._X_test)

benchmarks/benchmarks/bench_model.py

@@ -54,7 +54,6 @@
     "nipype",
     "nitime",
     "nitransforms",
-    "numpy",
     "pandas",
     "scipy",
     "seaborn",
@@ -154,20 +153,20 @@
 
 # -- Options for LaTeX output ------------------------------------------------
 
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #
-    # 'papersize': 'letterpaper',
-    # The font size ('10pt', '11pt' or '12pt').
-    #
-    # 'pointsize': '10pt',
-    # Additional stuff for the LaTeX preamble.
-    #
-    # 'preamble': '',
-    # Latex figure (float) alignment
-    #
-    # 'figure_align': 'htbp',
-}
+# latex_elements = {
+#     # The paper size ('letterpaper' or 'a4paper').
+#     #
+#     # 'papersize': 'letterpaper',
+#     # The font size ('10pt', '11pt' or '12pt').
+#     #
+#     # 'pointsize': '10pt',
+#     # Additional stuff for the LaTeX preamble.
+#     #
+#     # 'preamble': '',
+#     # Latex figure (float) alignment
+#     #
+#     # 'figure_align': 'htbp',
+# }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,

docs/conf.py

@@ -34,7 +34,7 @@
     "WORKDIR = Path.home() / \"tmp\" / \"nifreezedev\" / \"ismrm25\"\n",
     "WORKDIR.mkdir(parents=True, exist_ok=True)\n",
     "\n",
-    "OUTPUT_DIR = Path(\"/data/derivatives\") / \"nifreeze-ismrm25-exp2\"\n",
+    "OUTPUT_DIR = Path.home() / \"tmp\" / \"nifreezedev\" / \"ismrm25\" / \"nifreeze-ismrm25-exp2\"\n",
     "OUTPUT_DIR.mkdir(exist_ok=True, parents=True)"
    ]
   },