viz

Parameters

hz : GlobalHorizon instance act : fury.actor visual object

Parameters

tractogramssequence of StatefulTractograms

StatefulTractograms are used for making sure that the coordinate systems are correct

imagessequence of tuples

Each tuple contains data and affine

pamssequence of PeakAndMetrics

Contains peak directions and spherical harmonic coefficients

clusterbool

Enable QuickBundlesX clustering

cluster_thrfloat

Distance threshold used for clustering. Default value 15.0 for small animal data you may need to use something smaller such as 2.0. The threshold is in mm. For this parameter to be active cluster should be enabled.

random_colorsstring

Given multiple tractograms and/or ROIs then each tractogram and/or ROI will be shown with different color. If no value is provided both the tractograms and the ROIs will have a different random color generated from a distinguishable colormap. If the effect should only be applied to one of the 2 objects, then use the options ‘tracts’ and ‘rois’ for the tractograms and the ROIs respectively.

bg_colorndarray or list or tuple

Define the background color of the scene. Default is black (0, 0, 0)

order_transparentbool

Default True. Use depth peeling to sort transparent objects. If True also enables anti-aliasing.

length_gtfloat

Clusters with average length greater than length_gt amount in mm will be shown.

length_ltfloat

Clusters with average length less than length_lt amount in mm will be shown.

clusters_gtint

Clusters with size greater than clusters_gt will be shown.

clusters_ltint

Clusters with size less than clusters_lt will be shown.

world_coordsbool

Show data in their world coordinates (not native voxel coordinates) Default True.

interactivebool

Allow user interaction. If False then Horizon goes on stealth mode and just saves pictures.

buanbool, optional

Enables BUAN framework visualization. Default is False.

buan_colorslist, optional

List of colors for bundles.

roi_imagesbool, optional

Displays binary images as contours. Default is False.

roi_colorsndarray or list or tuple, optional

Define the color of the roi images. Default is red (1, 0, 0)

out_pngstring

Filename of saved picture.

recorded_eventsstring

File path to replay recorded events

return_showmbool

Return ShowManager object. Used only at Python level. Can be used for extending Horizon’s cababilities externally and for testing purposes.

References

Parameters

tractogramssequence of StatefulTractograms

StatefulTractograms are used for making sure that the coordinate systems are correct

imagessequence of tuples

Each tuple contains data and affine

pamssequence of PeakAndMetrics

Contains peak directions and spherical harmonic coefficients

clusterbool

Enable QuickBundlesX clustering

cluster_thrfloat

Distance threshold used for clustering. Default value 15.0 for small animal data you may need to use something smaller such as 2.0. The threshold is in mm. For this parameter to be active cluster should be enabled.

random_colorsstring

Given multiple tractograms and/or ROIs then each tractogram and/or ROI will be shown with different color. If no value is provided both the tractograms and the ROIs will have a different random color generated from a distinguishable colormap. If the effect should only be applied to one of the 2 objects, then use the options ‘tracts’ and ‘rois’ for the tractograms and the ROIs respectively.

bg_colorndarray or list or tuple

Define the background color of the scene. Default is black (0, 0, 0)

order_transparentbool

Default True. Use depth peeling to sort transparent objects. If True also enables anti-aliasing.

length_gtfloat

Clusters with average length greater than length_gt amount in mm will be shown.

length_ltfloat

Clusters with average length less than length_lt amount in mm will be shown.

clusters_gtint

Clusters with size greater than clusters_gt will be shown.

clusters_ltint

Clusters with size less than clusters_lt will be shown.

world_coordsbool

Show data in their world coordinates (not native voxel coordinates) Default True.

interactivebool

Allow user interaction. If False then Horizon goes on stealth mode and just saves pictures.

buanbool, optional

Enables BUAN framework visualization. Default is False.

buan_colorslist, optional

List of colors for bundles.

roi_imagesbool, optional

Displays binary images as contours. Default is False.

roi_colorsndarray or list or tuple, optional

Define the color of the roi images. Default is red (1, 0, 0)

out_pngstring

Filename of saved picture.

recorded_eventsstring

File path to replay recorded events

return_showmbool

Return ShowManager object. Used only at Python level. Can be used for extending Horizon’s cababilities externally and for testing purposes.

References

Parameters

text : str font_size : int bold : bool

Returns

label : TextBlock2D

Parameters

text : str font_size : int bold : bool

Returns

label : TextBlock2D

Parameters

scene : Scene iren : Interactor data : 3d ndarray affine : 4x4 ndarray world_coords : bool

If True then the affine is applied.

peaksPeaksAndMetrics

Default None

mem :

Returns

panel : Panel

Parameters

fitslist

List of fits to be compared.

mapslist

Names of attributes to be compared. Default: ‘rtop’.

transposebool, optional

If False, different fits are placed on different rows and different maps on different columns. If True, the order is transposed. If None, the figures are placed such that there are more columns than rows. Default: None.

fit_labelslist, optional

Labels for the different fitting routines. If None the fits are labeled by number. Default: None.

map_labelslist, optional

Labels for the different attributes. If None the attribute names are used. Default: None.

fit_kwargslist or dict, optional

A dict or list of dicts with imshow options for each fitting routine. The dicts are passed to imshow as keyword-argument pairs. Default: {}.

map_kwargslist or dict, optional

A dict or list of dicts with imshow options for each MAP-MRI scalar. The dicts are passed to imshow as keyword-argument pairs. Default: {}.

filenamestring, optional

Filename where the image will be saved. Default: None.

Parameters

gtqti fit object

The qti fit to be considered as ground truth

fit1qti fit object

First qti fit to be compared

fit2qti fit object

Second qti fit to be compared

masknp.ndarray

Boolean array indicating which voxels to retain for comparing the values

mapsarray-like, optional

QTI invariants to be compared

fitnamearray-like, optional

Names of the used QTI fitting routines

xlimitsarray-like, optional

X-Axis limits for the histograms visualization

disprangearray-like, optional

Display range for maps

sliceint, optional

Axial brain slice to be visualized

Parameters

xnp.ndarray

Integer array containing x-axis

shape_profilenp.ndarray

Float array containing bundlewarp displacement magnitudes along the length of the bundle

stdnp.ndarray

Float array containing standard deviations

Parameters

vertices(N,3) ndarray

unit vector points of the sphere

val: (N) ndarray

Function values.

axmpl axis, optional

If specified, draw onto this existing axis instead.

vmin, vmaxfloats

Values to cut the z

cmap : mpl colormap

cbar: Whether to add the color-bar to the figure

triang : Whether to display the plot triangulated as a pseudo-color plot.

boundary : Whether to draw the boundary around the projection in a black line

Returns

axaxis

Matplotlib figure axis

Examples

>>> from dipy.data import default_sphere
>>> verts = default_sphere.vertices
>>> ax = sph_project(verts.T, np.random.rand(len(verts.T))) 

Parameters

file_namestring

file name for saving the plot

titlestring

title of the plot

xinteger list

x-axis values to be plotted

yinteger list

y-axis values to be plotted

xlabelstring

label for x-axis

ylablestring

label for y-axis

Parameters

img0array, shape(R, C)

the image to be plotted on the red channel, to the left of the figure

img1array, shape(R, C)

the image to be plotted on the green channel, to the right of the figure

title0string (optional)

the title to be written on top of the image to the left. By default, no title is displayed.

title_midstring (optional)

the title to be written on top of the middle image. By default, no title is displayed.

title1string (optional)

the title to be written on top of the image to the right. By default, no title is displayed.

fnamestring (optional)

the file name to write the resulting figure. If None (default), the image is not saved.

fig_kwargs: extra parameters for saving figure, e.g. dpi=300.

Parameters

nrowsint

the number of squares to be drawn vertically

ncolsint

the number of squares to be drawn horizontally

deltaint

the size of each square of the grid. Each square is delta x delta pixels

Returns

latticearray, shape (R, C)

the image (2D array) of the segular lattice. The shape (R, C) of the array is given by R = 1 + (delta + 1) * nrows C = 1 + (delta + 1) * ncols

Parameters

mappingDiffeomorphicMap object

the diffeomorphic map to be drawn

deltaint, optional

the size (in pixels) of the squares of the regular lattice to be used to plot the warping effects. Each square will be delta x delta pixels. By default, the size will be 10 pixels.

fnamestring, optional

the name of the file the figure will be written to. If None (default), the figure will not be saved to disk.

direct_grid_shapetuple, shape (2,), optional

the shape of the grid image after being deformed by the direct transformation. By default, the shape of the deformed grid is the same as the grid of the displacement field, which is by default equal to the shape of the fixed image. In other words, the resulting deformed grid (deformed by the direct transformation) will normally have the same shape as the fixed image.

direct_grid2worldarray, shape (3, 3), optional

the affine transformation mapping the direct grid’s coordinates to physical space. By default, this transformation will correspond to the image-to-world transformation corresponding to the default direct_grid_shape (in general, if users specify a direct_grid_shape, they should also specify direct_grid2world).

inverse_grid_shapetuple, shape (2,), optional

the shape of the grid image after being deformed by the inverse transformation. By default, the shape of the deformed grid under the inverse transform is the same as the image used as “moving” when the diffeomorphic map was generated by a registration algorithm (so it corresponds to the effect of warping the static image towards the moving).

inverse_grid2worldarray, shape (3, 3), optional

the affine transformation mapping inverse grid’s coordinates to physical space. By default, this transformation will correspond to the image-to-world transformation corresponding to the default inverse_grid_shape (in general, if users specify an inverse_grid_shape, they should also specify inverse_grid2world).

show_figurebool, optional

if True (default), the deformed grids will be plotted using matplotlib, else the grids are just returned

fig_kwargs: extra parameters for saving figure, e.g. dpi=300.

Returns

warped_forwardarray

Image with the grid showing the effect of transforming the moving image to the static image. The shape will be direct_grid_shape if specified, otherwise the shape of the static image.

warped_backwardarray

Image with the grid showing the effect of transforming the static image to the moving image. Shape will be inverse_grid_shape if specified, otherwise the shape of the moving image.

Notes

The default value for the affine transformation is “-1” to handle the case in which the user provides “None” as input meaning “identity”. If we used None as default, we wouldn’t know if the user specifically wants to use the identity (specifically passing None) or if it was left unspecified, meaning to use the appropriate default matrix.

Parameters

Varray, shape (S, R, C)

the 3D volume to extract the slices from

slice_indicesarray, shape (3,) (optional)

the indices of the sagittal (slice_indices[0]), coronal (slice_indices[1]) and axial (slice_indices[2]) slices to be displayed. If None, the middle slices along each direction are displayed.

fnamestring (optional)

the name of the file to save the figure to. If None (default), the figure is not saved to disk.

fig_kwargs: extra parameters for saving figure, e.g. dpi=300.

Parameters

Larray, shape (S, R, C)

the first volume to extract the slice from plotted to the left

Rarray, shape (S, R, C)

the second volume to extract the slice from, plotted to the right

slice_indexint (optional)

the index of the slices (along the axis given by slice_type) to be overlaid. If None, the slice along the specified axis is used

slice_typeint (optional)

the type of slice to be extracted: 0=sagittal, 1=coronal (default), 2=axial.

ltitlestring (optional)

the string to be written as the title of the left image. By default, no title is displayed.

rtitlestring (optional)

the string to be written as the title of the right image. By default, no title is displayed.

fnamestring (optional)

the name of the file to write the image to. If None (default), the figure is not saved to disk.

fig_kwargs: extra parameters for saving figure, e.g. dpi=300.

Parameters

bundleslist

Bundles to be rendered.

interactiveboolean, optional

If True a 3D interactive rendering is created. Default is True.

viewstr, optional

Viewing angle. Supported options: ‘sagital’,’axial’ and ‘coronal’. Default is ‘sagital’.

colorslist, optional

Colors to be used for each bundle. If None default colors are used.

linewidthfloat, optional

Width of each rendered streamline. Default is 0.3.

save_asstr, optional

If not None rendered scene is stored in a png file with that name. Default is None.

Parameters

b1Streamlines

Bundle one to be rendered.

b2Streamlines

Bundle two to be rendered.

fname: str

Rendered scene is stored in a png file with that name.

C1tuple, optional

Color to be used for first bundle. Default red.

C2tuple, optional

Color to be used for second bundle. Default green.

interactiveboolean, optional

If True a 3D interactive rendering is created. Default is True.

Parameters

points_alignedList

List containing starting positions of vectors.

directionsList

List containing unitary directions of vectors.

colorsList

List containing colors for each vector.

offsetsList

List containing vector field modules.

fname: str

Rendered scene is stored in a png file with that name.

bundleStreamlines, optional

Bundle to be rendered with vector field (Default None).

interactiveboolean, optional

If True a 3D interactive rendering is created. Default is True.

Parameters

bundleStreamlines,

Bundle to be rendered.

offsetsList

List containing displacement magnitdues per point on the bundle.

fname: str

Rendered scene is stored in a png file with that name.

interactiveboolean, optional

If True a 3D interactive rendering is created. Default is True.