intensity_normalization.plot package

Submodules

intensity_normalization.plot.histogram module

Plot histogram of the intensities of a set of images Author: Jacob Reinhold <jcreinhold@gmail.com> Created on: 02 Jun 2021

class intensity_normalization.plot.histogram.HistogramPlotter(*, figsize: tuple[int, int] = (12, 10), alpha: float = 0.8, title: str | None = None)

Bases: DirectoryCLI

call_from_argparse_args(args: Namespace, /, **kwargs: Any) → None

static description() → str

classmethod from_argparse_args(args: Namespace) → HistogramPlotter

from_directories(image_dir: intnormt.PathLike, /, mask_dir: intnormt.PathLike | None = None, *, ext: str = 'nii*', exclude: collections.abc.Sequence[str] = ('membership',), **kwargs: Any) → plt.Axes

static fullname() → str

classmethod get_parent_parser(desc: str, valid_modalities: frozenset[str] = frozenset({'flair', 'md', 'other', 'pd', 't1', 't2'}), **kwargs: Any) → ArgumentParser

static name() → str

plot_all_histograms(images: collections.abc.Sequence[intnormt.ImageLike], /, masks: collections.abc.Sequence[intnormt.ImageLike] | None, **kwargs: Any) → plt.Axes

intensity_normalization.plot.histogram.plot_histogram(image: intnormt.ImageLike, /, mask: intnormt.ImageLike | None = None, *, ax: plt.Axes | None = None, n_bins: int = 200, log: bool = True, alpha: float = 0.8, linewidth: float = 3.0, **kwargs: Any) → plt.Axes

plots the histogram of the intensities of a numpy array within a given brain mask or estimated foreground mask (the estimate is just all intensities above the mean)

Parameters:

• image – image/array of interest

• mask – mask of the foreground, if none then assume skull-stripped

• ax – matplotlib ax to plot on, if none then create new ax

• n_bins – number of bins to use in histogram

• log – use log scale on the y-axis

• alpha – value in [0,1], controls opacity of line plot

• linewidth – width of line in histogram plot

• kwargs – arguments to the histogram function

Returns:

the ax the histogram is plotted on

Return type:

ax

Module contents