Added nifti2png

pyproject.toml

@@ -1,11 +1,28 @@
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
 [project]
 name = "open-dive"
 version = "0.1.0"
 description = "OpenDIVE (Open Diffusion Imaging Visualization for Everyone) is a command line interface tool for generating accessible, interpretable visualizations from diffusion MRI."
 readme = "README.md"
-requires-python = ">=3.13"
+requires-python = ">=3.10"
 dependencies = [
     "dipy>=1.10.0",
     "fury>=0.11.0",
 ]
-classifiers = ["Private :: Do Not Upload"]
+maintainers = [
+    {name = "Adam Saunders", email = "adam.m.saunders@vanderbilt.edu"},
+    {name = "Elyssa McMaster", email = "elyssa.m.mcmaster@vanderbilt.edu"}
+]
+keywords = ["diffusion MRI", "visualization", "medical imaging"]
+classifiers = ["Private :: Do Not Upload"]
+
+[project.urls]
+Repository = "https://github.com/MASILab/open_dive"
+Issues = "https://github.com/MASILab/open_dive/issues"
+
+
+[project.scripts]
+nifti2png = "open_dive.scripts.nifti2png:main"

src/open_dive/scripts/nifti2png.py

@@ -0,0 +1,59 @@
+import argparse
+from pathlib import Path
+
+from ..viz import plot_nifti
+
+
+def main():
+    # Create args
+    parser = argparse.ArgumentParser(description="Plot a slice of a NIFTI file")
+    parser.add_argument("nifti_path", type=Path, help="Path to NIFTI to plot")
+    parser.add_argument(
+        "-s", "--slice", default="m", help='Slice to plot or "m" for middle slice'
+    )
+    parser.add_argument(
+        "-o",
+        "--orientation",
+        default="axial",
+        help='Can be "axial", "sagittal" or "coronal"',
+    )
+    parser.add_argument(
+        "--size", default=(600, 400), help="Size of window, by default (600,400)"
+    )
+    parser.add_argument("--save_path", help="Optional path to save to")
+    parser.add_argument(
+        "--interactive",
+        action="store_true",
+        help="Whether to interactively show the scene",
+    )
+    parser.add_argument(
+        "--value_range",
+        type=int,
+        nargs=2,
+        help="Optional value range to pass to slicer. Default is min/max of image.",
+    )
+    parser.add_argument(
+        "--interpolation",
+        default="nearest",
+        help="Interpolation method to use (nearest or linear). Default is 'nearest'.",
+    )
+    parser.add_argument(
+        "--not_radiological",
+        action="store_true",
+        help="Do not plot in radiological view (i.e., subject right is on image right)",
+    )
+
+    args = parser.parse_args()
+
+    # Plot the NIFTI
+    plot_nifti(
+        args.nifti_path,
+        data_slice=args.slice,
+        orientation=args.orientation,
+        size=args.size,
+        radiological=not args.not_radiological,
+        save_path=args.save_path,
+        interactive=args.interactive,
+        value_range=args.value_range,
+        interpolation=args.interpolation,
+    )

src/open_dive/viz.py

@@ -0,0 +1,90 @@
+import nibabel as nib
+import numpy as np
+from dipy.viz import window
+from fury.actor import slicer
+
+
+def plot_nifti(
+    nifti_path,
+    data_slice="m",
+    orientation="axial",
+    size=(600, 400),
+    radiological=True,
+    save_path=None,
+    interactive=True,
+    **kwargs,
+):
+    """Create a 2D rendering of a NIFTI slice.
+
+    Parameters
+    ----------
+    nifti_path : str or Path
+        Path to NIFTI to plot
+    data_slice : str or int, optional
+        Slice to plot or "m" for middle slice, by default "m"
+    orientation : str, optional
+        Can be "axial", "sagittal" or "coronal", by default "axial"
+    size : tuple, optional
+        Size of window, by default (600,400)
+    radiological : bool, optional
+        Whether to plot in radiological view (subject right is on image left), by default True
+    save_path : str or Path, optional
+        Optional path to save to, by default None
+    interactive : bool, optional
+        Whether to interactively show the scene, by default True
+    **kwargs
+        Additional keyword arguments to pass to fury.actor.slicer
+    """
+
+    # Load the data and convert to RAS
+    nifti = nib.load(nifti_path)
+    nifti = nib.as_closest_canonical(nifti)
+
+    # Get the data and affine
+    data = nifti.get_fdata()
+    affine = nifti.affine
+
+    if radiological and orientation == "axial":
+        data = np.flip(data, axis=0)
+
+    # Set up slicer and window
+    slice_actor = slicer(data, affine=affine, **kwargs)
+    scene = window.Scene()
+    scene.add(slice_actor)
+
+    # Get slice if not defined
+    if orientation == "axial":
+        data_slice = data.shape[2] // 2 if data_slice == "m" else data_slice
+        slice_actor.display_extent(
+            0, data.shape[0], 0, data.shape[1], data_slice, data_slice
+        )
+
+        camera_pos = (0, 0, 1)
+        camera_up = (0, 1, 0)
+    elif orientation == "coronal":
+        data_slice = data.shape[1] // 2 if data_slice == "m" else data_slice
+        slice_actor.display_extent(
+            0, data.shape[0], data_slice, data_slice, 0, data.shape[2]
+        )
+
+        camera_pos = (0, 1, 0)
+        camera_up = (0, 0, 1)
+    elif orientation == "sagittal":
+        data_slice = data.shape[0] // 2 if data_slice == "m" else data_slice
+        slice_actor.display_extent(
+            data_slice, data_slice, 0, data.shape[1], 0, data.shape[2]
+        )
+
+        camera_pos = (1, 0, 0)
+        camera_up = (0, 0, 1)
+    camera_focal = (0, 0, 0)
+
+    # Set up camera
+    scene.set_camera(position=camera_pos, focal_point=camera_focal, view_up=camera_up)
+
+    # Show the scene
+    if save_path:
+        window.record(scene=scene, out_path=save_path, size=size, reset_camera=True)
+
+    if interactive:
+        window.show(scene, size=size, reset_camera=True)