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"""
=========================================
Tractography Clustering with QuickBundles
=========================================
This example explains how we can use QuickBundles
:footcite:p:`Garyfallidis2012a` to simplify/cluster streamlines.
First import the necessary modules.
"""
import numpy as np
from dipy.data import get_fnames
from dipy.io.pickles import save_pickle
from dipy.io.streamline import load_tractogram
from dipy.segment.clustering import QuickBundles
from dipy.viz import actor, colormap, window
###############################################################################
# For educational purposes we will try to cluster a small streamline bundle
# known from neuroanatomy as the fornix.
fname = get_fnames(name="fornix")
###############################################################################
# Load fornix streamlines.
fornix = load_tractogram(fname, "same", bbox_valid_check=False)
streamlines = fornix.streamlines
###############################################################################
# Perform QuickBundles clustering using the MDF metric and a 10mm distance
# threshold. Keep in mind that since the MDF metric requires streamlines to
# have the same number of points, the clustering algorithm will internally use
# a representation of streamlines that have been automatically
# downsampled/upsampled so they have only 12 points (To set manually the
# number of points, see :ref:`clustering-examples-ResampleFeature`).
qb = QuickBundles(threshold=10.0)
clusters = qb.cluster(streamlines)
###############################################################################
# `clusters` is a `ClusterMap` object which contains attributes that
# provide information about the clustering result.
print("Nb. clusters:", len(clusters))
print("Cluster sizes:", map(len, clusters))
print("Small clusters:", clusters < 10)
print("Streamlines indices of the first cluster:\n", clusters[0].indices)
print("Centroid of the last cluster:\n", clusters[-1].centroid)
###############################################################################
# `clusters` also has attributes such as `centroids` (cluster representatives),
# and methods like `add`, `remove`, and `clear` to modify the clustering
# result.
#
# Let's first show the initial dataset.
# Enables/disables interactive visualization
interactive = False
scene = window.Scene()
scene.SetBackground(1, 1, 1)
scene.add(actor.streamtube(streamlines, colors=window.colors.white))
window.record(scene=scene, out_path="fornix_initial.png", size=(600, 600))
if interactive:
window.show(scene)
###############################################################################
# .. rst-class:: centered small fst-italic fw-semibold
#
# Initial Fornix dataset.
#
#
# Show the centroids of the fornix after clustering (with random colors):
colormap = colormap.create_colormap(np.arange(len(clusters)))
scene.clear()
scene.SetBackground(1, 1, 1)
scene.add(actor.streamtube(streamlines, colors=window.colors.white, opacity=0.05))
scene.add(actor.streamtube(clusters.centroids, colors=colormap, linewidth=0.4))
window.record(scene=scene, out_path="fornix_centroids.png", size=(600, 600))
if interactive:
window.show(scene)
###############################################################################
# .. rst-class:: centered small fst-italic fw-semibold
#
# Showing the different QuickBundles centroids with random colors.
#
#
# Show the labeled fornix (colors from centroids).
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
scene.clear()
scene.SetBackground(1, 1, 1)
scene.add(actor.streamtube(streamlines, colors=colormap_full))
window.record(scene=scene, out_path="fornix_clusters.png", size=(600, 600))
if interactive:
window.show(scene)
###############################################################################
# .. rst-class:: centered small fst-italic fw-semibold
#
# Showing the different clusters.
#
#
# It is also possible to save the complete `ClusterMap` object with pickling.
save_pickle("QB.pkl", clusters)
###############################################################################
# Finally, here is a video of QuickBundles applied on a larger dataset.
#
# .. raw:: html
#
# <iframe width="420" height="315" src="https://www.youtube.com/embed/kstL7KKqu94" frameborder="0" allowfullscreen></iframe> # noqa: E501
#
#
# References
# ----------
#
# .. footbibliography::
#
|
