Merge pull request #101 from jhlegarreta/RelocatePlotDWIFromEddy

ENH: Add DWI volume plot method

.circleci/config.yml

@@ -20,6 +20,23 @@ jobs:
           name: Install package
           command: pip install .[test]
 
+      - restore_cache:
+          keys:
+            - apt-v0
+          paths:
+            - /var/lib/apt
+
+      - run:
+          name: Install texlive
+          command: |
+            sudo apt-get update
+            sudo apt-get install -y --no-install-recommends dvipng texlive texlive-latex-extra cm-super
+
+      - save_cache:
+         key: apt-v0
+         paths:
+            - /var/lib/apt
+
       - restore_cache:
           keys:
             - tf-v0

.github/workflows/build_test_deploy.yml

@@ -94,6 +94,17 @@ jobs:
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
 
+      - uses: actions/cache@v4
+        with:
+          path: /var/lib/apt
+          key: apt-cache-v0
+          restore-keys: |
+            apt-cache-v0
+      - name: Install tex
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y --no-install-recommends dvipng texlive texlive-latex-extra cm-super
+
       - name: Install package
         run: pip install $PACKAGE
       - name: Verify installation

nireports/reportlets/modality/dwi.py

@@ -21,10 +21,66 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Visualizations for diffusion MRI data."""
+import nibabel as nb
 import numpy as np
 import matplotlib as mpl
 from matplotlib import pyplot as plt
 from mpl_toolkits.mplot3d import art3d
+from nilearn.plotting import plot_anat
+
+
+def plot_dwi(dataobj, affine, gradient=None, **kwargs):
+    """
+    Plot orthogonal (axial, coronal, sagittal) slices of a given DWI volume. The
+    slices displayed are determined by a tuple contained in the ``cut_coords``
+    keyword argument.
+
+    Parameters
+    ----------
+    dataobj : :obj:`numpy.ndarray`
+        DWI volume data: a single 3D volume from a given gradient direction.
+    affine : :obj:`numpy.ndarray`
+        Affine transformation matrix.
+    gradient : :obj:`numpy.ndarray`
+        Gradient values in RAS+b format at the chosen gradient direction.
+    kwargs : :obj:`dict`
+        Extra args given to :obj:`nilearn.plotting.plot_anat()`.
+
+    Returns
+    -------
+    :class:`nilearn.plotting.displays.OrthoSlicer` or None
+        An instance of the OrthoSlicer class. If ``output_file`` is defined,
+        None is returned.
+
+    """
+
+    plt.rcParams.update(
+        {
+            "text.usetex": True,
+            "font.family": "sans-serif",
+            "font.sans-serif": ["Helvetica"],
+        }
+    )
+
+    affine = np.diag(nb.affines.voxel_sizes(affine).tolist() + [1])
+    affine[:3, 3] = -1.0 * (affine[:3, :3] @ ((np.array(dataobj.shape) - 1) * 0.5))
+
+    vmax = kwargs.pop("vmax", None) or np.percentile(dataobj, 98)
+    cut_coords = kwargs.pop("cut_coords", None) or (0, 0, 0)
+
+    return plot_anat(
+        nb.Nifti1Image(dataobj, affine, None),
+        vmax=vmax,
+        cut_coords=cut_coords,
+        title=(
+            r"Reference $b$=0"
+            if gradient is None
+            else f"""\
+$b$={gradient[3].astype(int)}, \
+$\\vec{{b}}$ = ({', '.join(str(v) for v in gradient[:3])})"""
+        ),
+        **kwargs,
+    )
 
 
 def plot_heatmap(

nireports/tests/data/ds000114_sub-01_ses-test_desc-trunc_dwi.bval

@@ -0,0 +1 @@
+0 0 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 

nireports/tests/data/ds000114_sub-01_ses-test_desc-trunc_dwi.bvec

@@ -0,0 +1,3 @@
+0 0 0 0 0 0 0 -1 -0.002 0.026 -0.591 0.236 0.893 -0.796 -0.234 -0.936 -0.506 -0.346 -0.457 0.487 
+0 0 0 0 0 0 0 0 1 0.649 -0.766 -0.524 -0.259 0.129 0.93 0.14 -0.845 -0.847 -0.631 -0.389 
+0 0 0 0 0 0 0 0 0 0.76 0.252 0.818 0.368 0.591 0.284 0.324 -0.175 -0.402 -0.627 0.782 

nireports/tests/test_dwi.py

@@ -23,11 +23,35 @@
 """Test DWI reportlets."""
 
 import pytest
+from pathlib import Path
 
+import nibabel as nb
 import numpy as np
 from matplotlib import pyplot as plt
 
-from nireports.reportlets.modality.dwi import plot_gradients
+from nireports.reportlets.modality.dwi import plot_dwi, plot_gradients
+
+
+def test_plot_dwi(tmp_path, testdata_path, outdir):
+    """Check the plot of DWI data."""
+
+    stem = 'ds000114_sub-01_ses-test_desc-trunc_dwi'
+    dwi_img = nb.load(testdata_path / f'{stem}.nii.gz')
+    affine = dwi_img.affine
+
+    bvecs = np.loadtxt(testdata_path / f'{stem}.bvec').T
+    bvals = np.loadtxt(testdata_path / f'{stem}.bval')
+
+    gradients = np.hstack([bvecs, bvals[:, None]])
+
+    # Pick a random volume to show
+    rng = np.random.default_rng(1234)
+    idx = rng.integers(low=0, high=dwi_img.shape[-1], size=1).item()
+
+    _ = plot_dwi(dwi_img.get_fdata()[..., idx], affine, gradient=gradients[idx])
+
+    if outdir is not None:
+        plt.savefig(outdir / f'{stem}.svg', bbox_inches='tight')
 
 
 @pytest.mark.parametrize(