neuroplot.plot.single.SinglePlot

class neuroplot.plot.single.SinglePlot(axes: int | Sequence[int] | None = None, slices: int | Sequence[int] | None = None, transforms: Sequence[Callable[[ndarray], ndarray]] | None = None, figsize: tuple[float, float] | None = None, title: str | None = None)

To plot a single neuroimage.

2D slices will be plotted via the method plot(). The user can choose which anatomical axes to plot, and which slice to plot along the axes.

The title of the figure can be changed between plots using set_title().

Just a random reference to Harris et al.[1]. And another to Matplotlib[2].

Parameters:

• axes (int | Sequence[int] | None, default=None) – The axis (or axes) to plot, among 0 (sagittal axis), 1 (coronal) or 2 (axial). Can be passed as a single axis, or a list of axes. If None, the three axes will be plotted.

• slices (int | Sequence[int] | None, default=None) – The slice to plot for each axis. If None, the middle slice will be plotted. Otherwise, the number of slices passed must be equal to the number of plotted axes (equal to \(3\) if axes=None).

• transforms (Sequence[Callable[[np.ndarray], np.ndarray]] | None, default=None) –

  Potential transforms to apply to the image before plotting. See neuroplot.transforms.

  Important

  No matter the transforms passed, the image will first be reoriented to the RAS+ coordinate system.

• figsize (tuple[float, float] | None, default=None) – The size of the figure. See matplotlib.pyplot.figure() for more details.

• title (str | None, default=None) – A potential title for the figures that will be plotted.

Raises:

AssertionError – If the number of slices passed is not equal to the number of plotted axes.

Examples

from neuroplot.plot.single import SinglePlot
from neuroplot.transforms import RescaleIntensity

plotter = SinglePlot(axes=[0, 2], slices=[55, 167], transforms=[RescaleIntensity()])

>>> plotter.set_title("A first image")
>>> plotter.plot("data/example_1.nii.gz")

>>> plotter.set_title("Another image")
>>> plotter.plot("data/example_2.nii.gz")

See also

neuroplot.plot.multiple.MultiplePlot

To plot multiple neuroimages in a grid of subplots.

References

[1]

Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel J. Smith, Robert Kern, Matti Picus, Stephan Hoyer, Marten H. van Kerkwijk, Matthew Brett, Allan Haldane, Jaime Fernández del Río, Mark Wiebe, Pearu Peterson, Pierre Gérard-Marchant, Kevin Sheppard, Tyler Reddy, Warren Weckesser, Hameer Abbasi, Christoph Gohlke, and Travis E. Oliphant. Array programming with NumPy. Nature, 585(7825):357–362, September 2020. URL: https://doi.org/10.1038/s41586-020-2649-2, doi:10.1038/s41586-020-2649-2.

[2]

J. D. Hunter. Matplotlib: a 2d graphics environment. Computing in Science & Engineering, 9(3):90–95, 2007. doi:10.1109/MCSE.2007.55.

plot(img_path: str | Path, show: bool = True) → Figure

Builds a plot of an image.

Parameters:

• img_path (Union[str, Path]) – The path to the image to plot.

• show (bool, default=True) – Whether to display the figure.

Returns:

matplotlib.figure.Figure – The figure with the desired 2D slices.

Raises:

IndexError – If a slice passed in slices is out of bounds in this image.

set_title(title: str | None) → None

To change the title of the future plot.

Parameters:

title (Optional[str]) – The new title.

Examples using neuroplot.plot.single.SinglePlot

Plot a 3D image

Plot a 3D image