Merge pull request #153 from effigies/typ/annotations

type: Relax Nifti1Image to SpatialImage

Author: jhlegarreta

nireports/reportlets/mosaic.py

@@ -38,6 +38,7 @@
 import numpy as np
 import numpy.typing as npt
 from matplotlib.gridspec import GridSpec
+from nibabel.spatialimages import SpatialImage
 from nilearn import image as nlimage
 from nilearn.plotting import plot_anat
 from svgutils.transform import SVGFigure, fromstring
@@ -55,9 +56,9 @@
 
 
 def plot_segs(
-    image_nii: ty.Union[str, nb.Nifti1Image],
-    seg_niis: list[ty.Union[str, nb.Nifti1Image]],
-    bbox_nii: ty.Union[str, nb.Nifti1Image, None] = None,
+    image_nii: ty.Union[str, SpatialImage],
+    seg_niis: list[ty.Union[str, SpatialImage]],
+    bbox_nii: ty.Union[str, SpatialImage, None] = None,
     masked: bool = False,
     compress: ty.Union[bool, L["auto"]] = "auto",
     **plot_params,
@@ -76,7 +77,7 @@ def plot_segs(
     image_nii = _3d_in_file(image_nii)
     canonical_r = rotation2canonical(image_nii)
     image_nii = rotate_affine(image_nii, rot=canonical_r)
-    seg_imgs: list[nb.Nifti1Image] = [
+    seg_imgs: list[SpatialImage] = [
         rotate_affine(_3d_in_file(f), rot=canonical_r) for f in seg_niis
     ]
     data = image_nii.get_fdata()
@@ -88,7 +89,7 @@ def plot_segs(
     )
 
     if masked:
-        bbox_nii: nb.Nifti1Image = nlimage.threshold_img(bbox_nii, 1e-3)  # type: ignore[no-redef]
+        bbox_nii: SpatialImage = nlimage.threshold_img(bbox_nii, 1e-3)  # type: ignore[no-redef]
 
     cuts = cuts_from_bbox(bbox_nii, cuts=7)
     out_files = []
@@ -104,14 +105,14 @@ def plot_segs(
 
 
 def plot_registration(
-    anat_nii: nb.spatialimages.SpatialImage,
+    anat_nii: SpatialImage,
     div_id: str,
     plot_params: ty.Union[dict[str, ty.Any], None] = None,
     order: tuple[L["x", "y", "z"], L["x", "y", "z"], L["x", "y", "z"]] = ("z", "x", "y"),
     cuts: ty.Union[dict[str, list[float]], None] = None,
     estimate_brightness: bool = False,
     label: ty.Union[str, None] = None,
-    contour: ty.Union[nb.spatialimages.SpatialImage, None] = None,
+    contour: ty.Union[SpatialImage, None] = None,
     compress: ty.Union[bool, L["auto"]] = "auto",
     dismiss_affine: bool = False,
 ) -> list[SVGFigure]:
@@ -184,8 +185,8 @@ def plot_registration(
 
 
 def _plot_anat_with_contours(
-    image: nb.Nifti1Image,
-    segs: ty.Union[list[nb.Nifti1Image], None] = None,
+    image: SpatialImage,
+    segs: ty.Union[list[SpatialImage], None] = None,
     compress: ty.Union[bool, L["auto"]] = "auto",
     **plot_params,
 ) -> str:
@@ -233,12 +234,12 @@ def plot_segmentation(anat_file: str, segmentation: str, out_file: str, **kwargs
     vmax = kwargs.get("vmax")
     vmin = kwargs.get("vmin")
 
-    anat_ras = nb.as_closest_canonical(load_api(anat_file, nb.spatialimages.SpatialImage))
+    anat_ras = nb.as_closest_canonical(load_api(anat_file, SpatialImage))
     anat_ras_plumb = anat_ras.__class__(
         anat_ras.dataobj, _dicom_real_to_card(anat_ras.affine), anat_ras.header
     )
 
-    seg_ras = nb.as_closest_canonical(load_api(segmentation, nb.spatialimages.SpatialImage))
+    seg_ras = nb.as_closest_canonical(load_api(segmentation, SpatialImage))
     seg_ras_plumb = seg_ras.__class__(
         seg_ras.dataobj, _dicom_real_to_card(seg_ras.affine), seg_ras.header
     )
@@ -430,8 +431,8 @@ def plot_spikes(
     """Plot a mosaic enhancing EM spikes."""
     from mpl_toolkits.axes_grid1 import make_axes_locatable
 
-    nii = nb.as_closest_canonical(load_api(in_file, nb.spatialimages.SpatialImage))
-    fft = load_api(in_file, nb.spatialimages.SpatialImage).get_fdata()
+    nii = nb.as_closest_canonical(load_api(in_file, SpatialImage))
+    fft = load_api(in_file, SpatialImage).get_fdata()
 
     data = nii.get_fdata()
     zooms = nii.header.get_zooms()[:2]

nireports/reportlets/utils.py

@@ -44,6 +44,7 @@
 import nibabel as nb
 import numpy as np
 import numpy.typing as npt
+from nibabel.spatialimages import SpatialImage
 from svgutils.transform import SVGFigure
 
 from ..tools.ndimage import load_api
@@ -269,7 +270,7 @@ def _bbox(img_data: npt.NDArray[G], bbox_data: npt.NDArray) -> npt.NDArray[G]:
     return img_data[ystart:ystop, xstart:xstop, zstart:zstop]
 
 
-def cuts_from_bbox(mask_nii: nb.Nifti1Image, cuts: int = 3) -> dict[str, list[float]]:
+def cuts_from_bbox(mask_nii: SpatialImage, cuts: int = 3) -> dict[str, list[float]]:
     """Find equi-spaced cuts for presenting images."""
     mask_data = np.asanyarray(mask_nii.dataobj) > 0.0
 
@@ -316,8 +317,8 @@ def cuts_from_bbox(mask_nii: nb.Nifti1Image, cuts: int = 3) -> dict[str, list[fl
 
 
 def _3d_in_file(
-    in_file: ty.Union[nb.Nifti1Image, str, os.PathLike, list[ty.Union[str, os.PathLike]]],
-) -> nb.Nifti1Image:
+    in_file: ty.Union[SpatialImage, str, os.PathLike, list[ty.Union[str, os.PathLike]]],
+) -> SpatialImage:
     """if self.inputs.in_file is 3d, return it.
     if 4d, pick an arbitrary volume and return that.
 
@@ -329,8 +330,8 @@ def _3d_in_file(
     if isinstance(in_file, list):
         in_file = in_file[0]
 
-    if not isinstance(in_file, nb.Nifti1Image):
-        in_file = load_api(in_file, nb.Nifti1Image)
+    if not isinstance(in_file, SpatialImage):
+        in_file = load_api(in_file, SpatialImage)
 
     if len(in_file.shape) == 3:
         return in_file