nanslice.layer module¶
layer.py
Contains the Layer
class and the blend_layers()
function.
-
class
nanslice.layer.
Layer
(image, scale=1.0, volume=0, interp_order=1, cmap=None, clim=None, label='', mask=None, mask_threshold=0, alpha=None, alpha_lim=None, alpha_scale=1.0, alpha_label='')[source]¶ Bases:
object
The Layer class
Each layer consists of a base MR image, with optional mask and alpha (transparency) images and their associated parameters (colormap, limits, scales etc.)
Constructor parameters:
- image – The image contained in this layer. Can be either a string/path to an image file or an nibabel image
- scale – A scaling factor to multiply all voxels in the image by
- volume – If reading a 4D file, specify which volume to use
- interp_order – Interpolation order. 1 is linear interpolation
- cmap – The colormap to apply to the Layer. Any valid matplotlib colormap
- clim – The limits (min, max) values to use for the colormap
- label – The label for this layer (used for colorbars)
- mask – A mask image to use with this layer
- mask_threshold – Apply a threshold (lower) to the mask
- alpha – An alpha (transparency) image to use with this layer
- alpha_lim – Specify the limits/window for the alpha image
- alpha_scale – Scaling factor for the alpha image
- alpha_label – Label for the alpha axis on alphabars
-
get_alpha
(slicer)[source]¶ Returns the alpha (transparency) slice for this Layer
Parameters:
- slicer – The
Slicer
object to slice this layer with
- slicer – The
-
get_color
(slicer)[source]¶ Returns a colorized slice through the base image contained in the Layer
Parameters:
- slicer – The
Slicer
object to slice this layer with
- slicer – The