seaborn_image.filterplot#

seaborn_image.filterplot(data, filt='gaussian', *, ax=None, cmap=None, vmin=None, vmax=None, alpha=None, origin=None, interpolation=None, robust=False, perc=(2, 98), diverging=False, dx=None, units=None, dimension=None, describe=False, cbar=True, orientation='v', cbar_log=False, cbar_label=None, cbar_ticks=None, showticks=False, despine=None, extent=None, **kwargs)#

Apply N-dimensional filters and plot the filterd data as 2-D image with options to add scalebar, colorbar, titles and configure similar to imgplot

Parameters:

  • data (array-like) – Image data. Supported array shapes are all matplotlib.pyplot.imshow array shapes

  • filt (str or callable, optional) – Filter name or function to be applied. Filter name can be a string from seaborn_image.implemented_filters or a callable filter. Defaults to “gaussian”.

  • ax (matplotlib.axes.Axes, optional) – Matplotlib axes to plot image on. If None, figure and axes are auto-generated, by default None

  • cmap (str or matplotlib.colors.Colormap, optional) – Colormap for image. Can be a seaborn-image colormap or default matplotlib colormaps or any other colormap converted to a matplotlib colormap, by default None

  • gray (bool, optional) – If True and data is RGB image, it will be converted to grayscale. If True and cmap is None, cmap will be set to “gray”, by default None

  • vmin (float, optional) – Minimum data value that colormap covers, by default None

  • vmax (float, optional) – Maximum data value that colormap covers, by default None

  • alpha (float or array-like, optional) – matplotlib.pyplot.imshow alpha blending value from 0 (transparent) to 1 (opaque), by default None

  • origin (str, optional) – Image origin, by default None

  • interpolation (str, optional) – matplotlib.pyplot.imshow interpolation method used, by default None

  • robust (bool, optional) – If True and vmin or vmax are None, colormap range is calculated based on the percentiles defined in perc parameter, by default False

  • perc (tuple or list, optional) – If robust is True, colormap range is calculated based on the percentiles specified instead of the extremes, by default (2, 98) - 2nd and 98th percentiles for min and max values

  • dx (float, optional) – Size per pixel of the image data. Specifying dx and units adds a scalebar to the image, by default None

  • diverging (bool, optional) – If True, vmax and vmin are adjusted so they have the same absolute value, making the diverging color maps show 0 at the middle.

  • units (str, optional) – Units of dx, by default None

  • dimension (str, optional) –

    dimension of dx and units, by default None Options include (similar to matplotlib_scalebar):

    • ”si” : scale bar showing km, m, cm, etc.

    • ”imperial” : scale bar showing in, ft, yd, mi, etc.

    • ”si-reciprocal” : scale bar showing 1/m, 1/cm, etc.

    • ”angle” : scale bar showing °, ʹ (minute of arc) or ʹʹ (second of arc)

    • ”pixel” : scale bar showing px, kpx, Mpx, etc.

  • describe (bool, optional) – Brief statistical description of the data, by default True

  • cbar (bool, optional) – Specify if a colorbar is to be added to the image, by default True. If data is RGB image, cbar is False

  • orientation (str, optional) –

    Specify the orientaion of colorbar, by default “v”. Options include :

    • ’h’ or ‘horizontal’ for a horizontal colorbar to the bottom of the image.

    • ’v’ or ‘vertical’ for a vertical colorbar to the right of the image.

  • cbar_log (bool, optional) – Log scale colormap and colorbar

  • cbar_label (str, optional) – Colorbar label, by default None

  • cbar_ticks (list, optional) – List of colorbar ticks, by default None

  • showticks (bool, optional) – Show image x-y axis ticks, by default False

  • despine (bool, optional) – Remove axes spines from image axes as well as colorbar axes, by default None

  • extent (floats (left, right, bottom, top), optional) – The bounding box in data coordinates that the image will fill. The image is stretched individually along x and y to fill the box.

  • **kwargs (optional) – Any additional parameters to be passed to the specific filt chosen. For instance, “sigma” or “size” or “mode” etc.

Returns:

Matplotlib axes where the image is drawn.

Return type:

matplotlib.axes.Axes

Raises:

  • TypeError – if filt is not a string type or callable function

  • NotImplementedError – if a filt that is not implemented is specified

  • TypeError – if describe is not a bool

Examples

Use default gaussian filter

>>> import seaborn_image as isns
>>> img = isns.load_image("polymer")
>>> isns.filterplot(img, sigma=3)
../_images/filterplot-1.png

Specify an image filter with specific parameters

>>> isns.filterplot(img, "percentile", percentile=35, size=10)
../_images/filterplot-2.png

filter can also be a function

>>> import scipy.ndimage as ndi
>>> isns.filterplot(img, ndi.gaussian_filter, sigma=2.5)
../_images/filterplot-3.png

Specify other image parameters for visualization along with the filter

>>> isns.filterplot(img, "sobel", dx=15, units="nm", cmap="acton")
../_images/filterplot-4.png