Add round() when loading NIfTI for atlas building

tests/test_atlas_builder.py

@@ -0,0 +1,85 @@
+import os
+import pytest
+import numpy as np
+import nibabel as nib
+import pyvista as pv
+from yabplot.atlas_builder import build_subcortical_atlas
+
+pv.OFF_SCREEN = True
+
+
+def _make_atlas_nifti(tmp_path, label_id, label_value, dtype=np.float64):
+    """Create a synthetic atlas NIfTI with a sphere of voxels set to label_value."""
+    shape = (20, 20, 20)
+    data = np.zeros(shape, dtype=dtype)
+    cz, cy, cx = 10, 10, 10
+    z, y, x = np.ogrid[:shape[0], :shape[1], :shape[2]]
+    region_mask = (z - cz) ** 2 + (y - cy) ** 2 + (x - cx) ** 2 <= 5 ** 2
+    data[region_mask] = label_value
+    path = str(tmp_path / f"atlas_{label_id}.nii.gz")
+    nib.save(nib.Nifti1Image(data, np.eye(4)), path)
+    return path
+
+
+def test_build_subcortical_atlas_creates_vtk_and_lut(tmp_path):
+    """Verify that VTK mesh and atlas_LUT.txt are created for a matching region."""
+    nii_path = _make_atlas_nifti(tmp_path, label_id=10, label_value=10.0)
+    out_dir = str(tmp_path / "out")
+
+    build_subcortical_atlas(nii_path, {10: "thalamus_l"}, out_dir, smooth_i=0)
+
+    assert os.path.isfile(os.path.join(out_dir, "thalamus_l.vtk"))
+    assert os.path.isfile(os.path.join(out_dir, "atlas_LUT.txt"))
+
+
+def test_build_subcortical_atlas_rounds_float_labels(tmp_path):
+    """Check that float-imprecise label values are correctly matched after .round().
+
+    NIfTI volumes often store integer labels as float32, which can lead to slight 
+    imprecision when read back as float64 (using, e.g., nibabel.load). For example, 
+    a label value of 10.0 stored as float32 may be read back as 10.000000953674316 in float64.
+    Without .round(), the mask `data == rid` misses these voxels and produces no mesh. 
+    This test confirms the rounding fix is in effect.
+
+    """
+    # float32(10) + float32(1e-6) → 10.000001 in float32 → 10.000000953674316 in float64
+    label_value = np.float32(10.0) + np.float32(1e-6)
+    nii_path = _make_atlas_nifti(tmp_path, label_id=10, label_value=label_value, dtype=np.float32)
+
+    # Confirm the fixture actually has float-imprecise values (not exactly 10)
+    loaded_vals = np.unique(nib.load(nii_path).get_fdata())
+    loaded_vals = loaded_vals[loaded_vals != 0]
+    assert not np.all(loaded_vals == 10), (
+        "fixture should have float-imprecise label values to test rounding"
+    )
+
+    out_dir = str(tmp_path / "out")
+    build_subcortical_atlas(nii_path, {10: "thalamus_l"}, out_dir, smooth_i=0)
+
+    assert os.path.isfile(os.path.join(out_dir, "thalamus_l.vtk")), (
+        "thalamus_l.vtk not created — .round() may be missing from the get_fdata() call"
+    )
+
+
+def test_build_subcortical_atlas_missing_region_skips(tmp_path):
+    """Verify that a label absent from the volume produces no VTK file."""
+    nii_path = _make_atlas_nifti(tmp_path, label_id=10, label_value=10.0)
+    out_dir = str(tmp_path / "out")
+
+    build_subcortical_atlas(nii_path, {99: "phantom"}, out_dir, smooth_i=0)
+
+    assert not os.path.isfile(os.path.join(out_dir, "phantom.vtk"))
+
+
+def test_build_subcortical_atlas_both_filters_raises(tmp_path):
+    """Verify that providing both include_list and exclude_list raises ValueError."""
+    nii_path = _make_atlas_nifti(tmp_path, label_id=10, label_value=10.0)
+
+    with pytest.raises(ValueError):
+        build_subcortical_atlas(
+            nii_path,
+            {10: "thalamus_l"},
+            str(tmp_path / "out"),
+            include_list=["thalamus"],
+            exclude_list=["cerebellum"],
+        )

yabplot/atlas_builder.py

@@ -289,7 +289,7 @@ def build_subcortical_atlas(nii_path, labels_dict, out_dir, include_list=None, e
 
     # load the nifti volume and its affine matrix
     img = nib.load(nii_path)
-    data = img.get_fdata()
+    data = img.get_fdata().round()
     affine = img.affine
 
     # loop through targets, extract meshes, and save