viz

Download icons for fury

Return package-like thing and module setup for package name

Parameters

namestr

package name

trip_msgNone or str

message to give when someone tries to use the return package, but we could not import it, and have returned a TripWire object instead. Default message if None.

Returns

pkg_likemodule or TripWire instance

If we can import the package, return it. Otherwise return an object raising an error when accessed

have_pkgbool

True if import for package was successful, false otherwise

module_setupfunction

callable usually set as setup_module in calling namespace, to allow skipping tests.

Examples

Typical use would be something like this at the top of a module using an optional package:

>>> from dipy.utils.optpkg import optional_package
>>> pkg, have_pkg, setup_module = optional_package('not_a_package')

Of course in this case the package doesn’t exist, and so, in the module:

>>> have_pkg
False

and

>>> pkg.some_function() 
Traceback (most recent call last):
    ...
TripWireError: We need package not_a_package for these functions, but
``import not_a_package`` raised an ImportError

If the module does exist - we get the module

>>> pkg, _, _ = optional_package('os')
>>> hasattr(pkg, 'path')
True

Or a submodule if that’s what we asked for

>>> subpkg, _, _ = optional_package('os.path')
>>> hasattr(subpkg, 'dirname')
True

Read specific icon from specific style.

Parameters

stylestr

Current icon style. Default is icomoon.

fnamestr

Filename of icon. This should be found in folder HOME/.fury/style/. Default is infinity.png.

Returns

pathstr

Complete path of icon.

Simple utility function to build labels

Parameters

textstr

font_sizeint

boldbool

Returns

labelTextBlock2D

Generate colors that are maximally perceptually distinct.

This function generates a set of colors which are distinguishable by reference to the “Lab” color space, which more closely matches human color perception than RGB. Given an initial large list of possible colors, it iteratively chooses the entry in the list that is farthest (in Lab space) from all previously-chosen entries. While this “greedy” algorithm does not yield a global maximum, it is simple and efficient. Moreover, the sequence of colors is consistent no matter how many you request, which facilitates the users’ ability to learn the color order and avoids major changes in the appearance of plots when adding or removing lines.

Parameters

bgtuple (optional)

Background RGB color, to make sure that your colors are also distinguishable from the background. Default: (0, 0, 0).

excludelist of tuples (optional)

Additional RGB colors to be distinguishable from.

nb_colorsint (optional)

Number of colors desired. Default: generate as many colors as needed.

Returns

iterable of ndarray

If nb_colors is provided, returns a list of RBG colors. Otherwise, yields the next RBG color maximally perceptually distinct from previous ones.

Notes

Code was initially in matlab and was rewritten in Python for dipy by the Dipy Team. Thank you Tim Holy for putting this online. Visit http://www.mathworks.com/matlabcentral/fileexchange/29702 for the original implementation (v1.2), 14 Dec 2010 (Updated 07 Feb 2011).

Examples

>>> from dipy.viz.colormap import distinguishable_colormap
>>> # Generate 5 colors
>>> [c for i, c in zip(range(5), distinguishable_colormap())]
[array([ 0.,  1.,  0.]),
 array([ 1.,  0.,  1.]),
 array([ 1.        ,  0.75862069,  0.03448276]),
 array([ 0.        ,  1.        ,  0.89655172]),
 array([ 0.        ,  0.17241379,  1.        ])]

Interactive medical visualization - Invert the Horizon!

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_colorsbool

Given multiple tractograms have been included then each tractogram will be shown with different color

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.

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

Horizon_ISMRM19

Garyfallidis E., M-A. Cote, B.Q. Chandio, S. Fadnavis, J. Guaje, R. Aggarwal, E. St-Onge, K.S. Juneja, S. Koudoro, D. Reagan, DIPY Horizon: fast, modular, unified and adaptive visualization, Proceedings of: International Society of Magnetic Resonance in Medicine (ISMRM), Montreal, Canada, 2019.

Euclidean length of streamlines

Length is in mm only if streamlines are expressed in world coordinates.

Parameters

streamlinesndarray or a list or dipy.tracking.Streamlines

If ndarray, must have shape (N,3) where N is the number of points of the streamline. If list, each item must be ndarray shape (Ni,3) where Ni is the number of points of streamline i. If dipy.tracking.Streamlines, its common_shape must be 3.

Returns

lengthsscalar or ndarray shape (N,)

If there is only one streamline, a scalar representing the length of the streamline. If there are several streamlines, ndarray containing the length of every streamline.

Examples

>>> from dipy.tracking.streamline import length
>>> import numpy as np
>>> streamline = np.array([[1, 1, 1], [2, 3, 4], [0, 0, 0]])
>>> expected_length = np.sqrt([1+2**2+3**2, 2**2+3**2+4**2]).sum()
>>> length(streamline) == expected_length
True
>>> streamlines = [streamline, np.vstack([streamline, streamline[::-1]])]
>>> expected_lengths = [expected_length, 2*expected_length]
>>> lengths = [length(streamlines[0]), length(streamlines[1])]
>>> np.allclose(lengths, expected_lengths)
True
>>> length([])
0.0
>>> length(np.array([[1, 2, 3]]))
0.0

Return package-like thing and module setup for package name

Parameters

namestr

package name

trip_msgNone or str

message to give when someone tries to use the return package, but we could not import it, and have returned a TripWire object instead. Default message if None.

Returns

pkg_likemodule or TripWire instance

If we can import the package, return it. Otherwise return an object raising an error when accessed

have_pkgbool

True if import for package was successful, false otherwise

module_setupfunction

callable usually set as setup_module in calling namespace, to allow skipping tests.

Examples

Typical use would be something like this at the top of a module using an optional package:

>>> from dipy.utils.optpkg import optional_package
>>> pkg, have_pkg, setup_module = optional_package('not_a_package')

Of course in this case the package doesn’t exist, and so, in the module:

>>> have_pkg
False

and

>>> pkg.some_function() 
Traceback (most recent call last):
    ...
TripWireError: We need package not_a_package for these functions, but
``import not_a_package`` raised an ImportError

If the module does exist - we get the module

>>> pkg, _, _ = optional_package('os')
>>> hasattr(pkg, 'path')
True

Or a submodule if that’s what we asked for

>>> subpkg, _, _ = optional_package('os.path')
>>> hasattr(subpkg, 'dirname')
True

Run QuickBundlesX and then run again on the centroids of the last layer

Running again QuickBundles at a layer has the effect of merging some of the clusters that maybe originally devided because of branching. This function help obtain a result at a QuickBundles quality but with QuickBundlesX speed. The merging phase has low cost because it is applied only on the centroids rather than the entire dataset.

Parameters

streamlinesStreamlines

thresholdssequence

List of distance thresholds for QuickBundlesX.

nb_ptsint

Number of points for discretizing each streamline

select_randomlyint

Randomly select a specific number of streamlines. If None all the streamlines are used.

rngRandomState

If None then RandomState is initialized internally.

verbosebool, optional.

If True, log information. Default False.

Returns

——-

clustersobj

Contains the clusters of the last layer of QuickBundlesX after merging.

References

Garyfallidis12

Garyfallidis E. et al., QuickBundles a method for tractography simplification, Frontiers in Neuroscience, vol 6, no 175, 2012.

Garyfallidis16

Garyfallidis E. et al. QuickBundlesX: Sequential clustering of millions of streamlines in multiple levels of detail at record execution time. Proceedings of the, International Society of Magnetic Resonance in Medicine (ISMRM). Singapore, 4187, 2016.

Save the stateful tractogram in any format (trk, tck, vtk, fib, dpy)

Parameters

sftStatefulTractogram

The stateful tractogram to save

filenamestring

Filename with valid extension

bbox_valid_checkbool

Verification for negative voxel coordinates or values above the volume dimensions. Default is True, to enforce valid file.

Returns

outputbool

True if the saving operation was successful

Slicer panel with slicer included

Parameters

sceneScene

irenInteractor

data3d ndarray

affine4x4 ndarray

world_coordsbool

If True then the affine is applied.

peaksPeaksAndMetrics

Default None

mem :

Returns

panelPanel

Simple utility function to build labels

Parameters

textstr

font_sizeint

boldbool

Returns

labelTextBlock2D

Return package-like thing and module setup for package name

Parameters

namestr

package name

trip_msgNone or str

message to give when someone tries to use the return package, but we could not import it, and have returned a TripWire object instead. Default message if None.

Returns

pkg_likemodule or TripWire instance

If we can import the package, return it. Otherwise return an object raising an error when accessed

have_pkgbool

True if import for package was successful, false otherwise

module_setupfunction

callable usually set as setup_module in calling namespace, to allow skipping tests.

Examples

Typical use would be something like this at the top of a module using an optional package:

>>> from dipy.utils.optpkg import optional_package
>>> pkg, have_pkg, setup_module = optional_package('not_a_package')

Of course in this case the package doesn’t exist, and so, in the module:

>>> have_pkg
False

and

>>> pkg.some_function() 
Traceback (most recent call last):
    ...
TripWireError: We need package not_a_package for these functions, but
``import not_a_package`` raised an ImportError

If the module does exist - we get the module

>>> pkg, _, _ = optional_package('os')
>>> hasattr(pkg, 'path')
True

Or a submodule if that’s what we asked for

>>> subpkg, _, _ = optional_package('os.path')
>>> hasattr(subpkg, 'dirname')
True

Slicer panel with slicer included

Parameters

sceneScene

irenInteractor

data3d ndarray

affine4x4 ndarray

world_coordsbool

If True then the affine is applied.

peaksPeaksAndMetrics

Default None

mem :

Returns

panelPanel

Decorator replaces custom skip test markup in doctests.

Say a function has a docstring:

>>> something # skip if not HAVE_AMODULE
>>> something + else
>>> something # skip if HAVE_BMODULE

This decorator will evaluate the expresssion after skip if. If this evaluates to True, then the comment is replaced by # doctest: +SKIP. If False, then the comment is just removed. The expression is evaluated in the globals scope of func.

For example, if the module global HAVE_AMODULE is False, and module global HAVE_BMODULE is False, the returned function will have docstring:

>>> something 
>>> something + else
>>> something

Return package-like thing and module setup for package name

Parameters

namestr

package name

trip_msgNone or str

message to give when someone tries to use the return package, but we could not import it, and have returned a TripWire object instead. Default message if None.

Returns

pkg_likemodule or TripWire instance

If we can import the package, return it. Otherwise return an object raising an error when accessed

have_pkgbool

True if import for package was successful, false otherwise

module_setupfunction

callable usually set as setup_module in calling namespace, to allow skipping tests.

Examples

Typical use would be something like this at the top of a module using an optional package:

>>> from dipy.utils.optpkg import optional_package
>>> pkg, have_pkg, setup_module = optional_package('not_a_package')

Of course in this case the package doesn’t exist, and so, in the module:

>>> have_pkg
False

and

>>> pkg.some_function() 
Traceback (most recent call last):
    ...
TripWireError: We need package not_a_package for these functions, but
``import not_a_package`` raised an ImportError

If the module does exist - we get the module

>>> pkg, _, _ = optional_package('os')
>>> hasattr(pkg, 'path')
True

Or a submodule if that’s what we asked for

>>> subpkg, _, _ = optional_package('os.path')
>>> hasattr(subpkg, 'dirname')
True

Draw a signal on a 2D projection of the sphere.

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

cmapmpl colormap

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

triangWhether to display the plot triangulated as a pseudo-color plot.

boundaryWhether 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))) 

Create a regular lattice of nrows x ncols squares.

Creates an image (2D array) of a regular lattice of nrows x ncols squares. The size of each square is delta x delta pixels (not counting the separation lines). The lines are one pixel width.

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

Return package-like thing and module setup for package name

Parameters

namestr

package name

trip_msgNone or str

message to give when someone tries to use the return package, but we could not import it, and have returned a TripWire object instead. Default message if None.

Returns

pkg_likemodule or TripWire instance

If we can import the package, return it. Otherwise return an object raising an error when accessed

have_pkgbool

True if import for package was successful, false otherwise

module_setupfunction

callable usually set as setup_module in calling namespace, to allow skipping tests.

Examples

Typical use would be something like this at the top of a module using an optional package:

>>> from dipy.utils.optpkg import optional_package
>>> pkg, have_pkg, setup_module = optional_package('not_a_package')

Of course in this case the package doesn’t exist, and so, in the module:

>>> have_pkg
False

and

>>> pkg.some_function() 
Traceback (most recent call last):
    ...
TripWireError: We need package not_a_package for these functions, but
``import not_a_package`` raised an ImportError

If the module does exist - we get the module

>>> pkg, _, _ = optional_package('os')
>>> hasattr(pkg, 'path')
True

Or a submodule if that’s what we asked for

>>> subpkg, _, _ = optional_package('os.path')
>>> hasattr(subpkg, 'dirname')
True

Plot two images one on top of the other using red and green channels.

Creates a figure containing three images: the first image to the left plotted on the red channel of a color image, the second to the right plotted on the green channel of a color image and the two given images on top of each other using the red channel for the first image and the green channel for the second one. It is assumed that both images have the same shape. The intended use of this function is to visually assess the quality of a registration result.

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`.

Plot three overlaid slices from the given volumes.

Creates a figure containing three images: the gray scale k-th slice of the first volume (L) to the left, where k=slice_index, the k-th slice of the second volume (R) to the right and the k-th slices of the two given images on top of each other using the red channel for the first volume and the green channel for the second one. It is assumed that both volumes have the same shape. The intended use of this function is to visually assess the quality of a registration result.

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=sagital, 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`.

Draw the effect of warping a regular lattice by a diffeomorphic map.

Draws a diffeomorphic map by showing the effect of the deformation on a regular grid. The resulting figure contains two images: the direct transformation is plotted to the left, and the inverse transformation is plotted to the right.

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.

Plot 3 slices from the given volume: 1 sagital, 1 coronal and 1 axial

Creates a figure showing the axial, coronal and sagittal slices at the requested positions of the given volume. The requested slices are specified by slice_indices.

Parameters

Varray, shape (S, R, C)

the 3D volume to extract the slices from

slice_indicesarray, shape (3,) (optional)

the indices of the sagital (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`.

Saves the simple plot with given x and y values

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