From a0aed25f6218e9f5dc269cf8d0bd0d1290806452 Mon Sep 17 00:00:00 2001 From: niksirbi Date: Mon, 21 Oct 2024 17:27:18 +0100 Subject: [PATCH] removed unnecessary voxel_sizes parameter --- brainglobe_template_builder/plots.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/brainglobe_template_builder/plots.py b/brainglobe_template_builder/plots.py index 8cf515b..d85e323 100644 --- a/brainglobe_template_builder/plots.py +++ b/brainglobe_template_builder/plots.py @@ -9,7 +9,6 @@ def plot_orthographic( img: np.ndarray, anat_space: str = "ASR", - voxel_sizes: tuple[float, float, float] = (1.0, 1.0, 1.0), show_slices: tuple[int, int, int] | None = None, mip_attenuation: float = 0.01, save_path: Path | None = None, @@ -17,8 +16,9 @@ def plot_orthographic( ) -> tuple[plt.Figure, np.ndarray]: """Plot image volume in three orthogonal views, plus a surface rendering. - The surface rendering is a maximum intensity projection (MIP) along the - vertical (superior-inferior) axis and is shown from the top. + The function assumes isotropic voxels (otherwise the proportions of the + image will be distorted). The surface rendering is a maximum intensity + projection (MIP) along the vertical (superior-inferior) axis. Parameters ---------- @@ -27,9 +27,6 @@ def plot_orthographic( anat_space : str, optional Anatomical space of of the image volume according to the Brainglobe definition (origin and order of axes), by default "ASR". - voxel_sizes : tuple, optional - Voxels sizes in micrometers per dimension, by default (1.0, 1.0, 1.0). - The relative sizes of the axes will be preserved in the plot. show_slices : tuple, optional Which slice to show per dimension. If None (default), show the middle slice along each dimension.