def show_tract(segmented_tract, color_positive, segmented_tract_negative,
color_negative, out_path):
"""Visualization of the segmented tract.
"""
affine = utils.affine_for_trackvis(voxel_size=np.array([1.25, 1.25, 1.25]))
bundle_native = transform_streamlines(segmented_tract,
np.linalg.inv(affine))
bundle_nativeNeg = transform_streamlines(segmented_tract_negative,
np.linalg.inv(affine))
renderer = window.Renderer()
stream_actor2 = actor.line(bundle_native,
colors=color_positive,
linewidth=0.1)
stream_actorNeg = actor.line(bundle_nativeNeg,
colors=color_negative,
opacity=0.01,
linewidth=0.1)
renderer.set_camera(position=(408.85, -26.23, 92.12),
focal_point=(0.42, -14.03, 0.82),
view_up=(-0.09, 0.85, 0.51))
bar = actor.scalar_bar()
renderer.add(stream_actor2)
renderer.add(stream_actorNeg)
renderer.add(bar)
window.show(renderer, size=(1920, 1039), reset_camera=False)
renderer.camera_info()
"""Take a snapshot of the window and save it
"""
window.record(renderer, out_path=out_path, size=(1920, 1039))
def voxelCount():
tractography, header = trackvis.read(T_A_filename)
tractography = [streamline[0] for streamline in tractography]
affine = utils.affine_for_trackvis(voxel_size=np.array([2, 2, 2]))
print("---Number of voxel---")
print(len(streamline_mapping(T_A, affine=affine).keys()))
tkinter.messagebox.showinfo(
"Voxel", len(streamline_mapping(T_A, affine=affine).keys()))
def show_tract(segmented_tract, color):
"""Visualization of the segmented tract.
"""
affine=utils.affine_for_trackvis(voxel_size=np.array([1.25,1.25,1.25]))
bundle_native = transform_streamlines(segmented_tract, np.linalg.inv(affine))
renderer = window.Renderer()
stream_actor = actor.line(bundle_native, linewidth=0.1)
bar = actor.scalar_bar()
renderer.add(stream_actor)
renderer.add(bar)
window.show(renderer, size=(600, 600), reset_camera=False)
"""Take a snapshot of the window and save it
"""
window.record(renderer, out_path='bundle2.1.png', size=(600, 600))
def convert_fibs(inp, outp, parcellation):
label_nii = nib.load(parcellation)
label_data = label_nii.get_data()
fiber_npz = np.load(inp)
fibers = fiber_npz[fiber_npz.keys()[0]]
voxel_size = label_nii.header.get_zooms()
shape = label_data.shape
affine = label_nii.affine
trackvis_header = nib.trackvis.empty_header()
trackvis_header['voxel_size'] = voxel_size
trackvis_header['dim'] = shape
trackvis_header['voxel_order'] = "RAS"
trackvis_point_space = utils.affine_for_trackvis(voxel_size)
trk = utils.move_streamlines(fibers, trackvis_point_space, input_space=np.eye(4))
trk = list(trk)
for_save = [(sl, None, None) for sl in trk]
nib.trackvis.write(outp, for_save, trackvis_header)
import nibabel as nib
# Save density map
dm_img = nib.Nifti1Image(dm.astype("int16"), hardi_img.affine)
dm_img.to_filename("lr-superiorfrontal-dm.nii.gz")
# Make a trackvis header so we can save streamlines
voxel_size = labels_img.header.get_zooms()
trackvis_header = nib.trackvis.empty_header()
trackvis_header['voxel_size'] = voxel_size
trackvis_header['dim'] = shape
trackvis_header['voxel_order'] = "RAS"
# Move streamlines to "trackvis space"
trackvis_point_space = utils.affine_for_trackvis(voxel_size)
lr_sf_trk = utils.move_streamlines(lr_superiorfrontal_track,
trackvis_point_space,
input_space=affine)
lr_sf_trk = list(lr_sf_trk)
# Save streamlines
for_save = [(sl, None, None) for sl in lr_sf_trk]
nib.trackvis.write("lr-superiorfrontal.trk", for_save, trackvis_header)
"""
Let's take a moment here to consider the representation of streamlines used in
dipy. Streamlines are a path though the 3d space of an image represented by a
set of points. For these points to have a meaningful interpretation, these
points must be given in a known coordinate system. The ``affine`` attribute of
the ``streamline_generator`` object specifies the coordinate system of the
points with respect to the voxel indices of the input data.
T_A_filename = 'F:\Thesis\Resources\\alldata\\201111_uf.right.trk'
threshold_short_streamlines = 0.0
color=colors.red
T_A, hdr = loadtrkfile(T_A_filename, threshold_short_streamlines=threshold_short_streamlines)
countstreamlines()
showhistogram()
tractography,header=trackvis.read(T_A_filename)
tractography = [streamline[0] for streamline in tractography]
affine=utils.affine_for_trackvis(voxel_size=np.array([2,2,2]))
print ("---Number of voxel---")
print (len(streamline_mapping(T_A,affine=affine).keys()))
show_tract(T_A, color)
def test_affine_for_trackvis():
voxel_size = np.array([1., 2, 3.])
affine = affine_for_trackvis(voxel_size)
origin = np.dot(affine, [0, 0, 0, 1])
assert_array_almost_equal(origin[:3], voxel_size / 2)
def test_affine_for_trackvis():
voxel_size = np.array([1., 2, 3.])
affine = affine_for_trackvis(voxel_size)
origin = np.dot(affine, [0, 0, 0, 1])
assert_array_almost_equal(origin[:3], voxel_size / 2)
def label_streamlines_density(streamlines, labels, affine, f_name, img,
label_img):
"""
.. figure:: connectivity.png
:align: center
**Connectivity of Corpus Callosum**
.. include:: ../links_names.inc
"""
shape = labels.shape
dm = utils.density_map(streamlines, shape, affine=affine)
sum = 0
count = 0
for i in dm:
for j in i:
for k in j:
if (k != 0):
sum = sum + k
count += 1
density = sum * 1.0 / count
print density
"""
To do that, we will use tools available in [nibabel](http://nipy.org/nibabel)
"""
# Save density map
dm_img = nib.Nifti1Image(dm.astype("int16"), img.get_affine())
dm_img.to_filename(f_name + "-dm.nii.gz")
# Make a trackvis header so we can save streamlines
voxel_size = label_img.get_header().get_zooms()
trackvis_header = nib.trackvis.empty_header()
trackvis_header['voxel_size'] = voxel_size
trackvis_header['dim'] = shape
trackvis_header['voxel_order'] = "RAS"
# Move streamlines to "trackvis space"
trackvis_point_space = utils.affine_for_trackvis(voxel_size)
lr_sf_trk = utils.move_streamlines(streamlines,
trackvis_point_space,
input_space=affine)
lr_sf_trk = list(lr_sf_trk)
"""
# Save streamlines
for_save = [(sl, None, None) for sl in lr_sf_trk]
nib.trackvis.write(f_name+"_label1.trk", for_save, trackvis_header)
"""
"""
import tractconverter as tc
density_file = f_name+"_label1.trk"
input_format=tc.detect_format(density_file)
input=input_format(density_file)
output=tc.FORMATS['vtk'].create(density_file+".vtk",input.hdr)
tc.convert(input,output)
"""
"""
Let's take a moment here to consider the representation of streamlines used in
dipy. Streamlines are a path though the 3d space of an image represented by a
set of points. For these points to have a meaningful interpretation, these
points must be given in a known coordinate system. The ``affine`` attribute of
the ``streamline_generator`` object specifies the coordinate system of the
points with respect to the voxel indices of the input data.
``trackvis_point_space`` specifies the trackvis coordinate system with respect
to the same indices. The ``move_streamlines`` function returns a new set of
streamlines from an existing set of streamlines in the target space. The
target space and the input space must be specified as affine transformations
with respect to the same reference [#]_. If no input space is given, the input
space will be the same as the current representation of the streamlines, in
other words the input space is assumed to be ``np.eye(4)``, the 4-by-4 identity
matrix.
All of the functions above that allow streamlines to interact with volumes take
an affine argument. This argument allows these functions to work with
streamlines regardless of their coordinate system. For example even though we
moved our streamlines to "trackvis space", we can still compute the density map
as long as we specify the right coordinate system.
"""
dm_trackvis = utils.density_map(lr_sf_trk,
shape,
affine=trackvis_point_space)
assert np.all(dm == dm_trackvis)
return dm, density
"""
This means that streamlines can interact with any image volume, for example a
high resolution structural image, as long as one can register that image to
the diffusion images and calculate the coordinate system with respect to that
image.
"""
"""
import nibabel as nib
# Save density map
dm_img = nib.Nifti1Image(dm.astype("int16"), hardi_img.get_affine())
dm_img.to_filename("lr-superiorfrontal-dm.nii.gz")
# Make a trackvis header so we can save streamlines
voxel_size = labels_img.get_header().get_zooms()
trackvis_header = nib.trackvis.empty_header()
trackvis_header['voxel_size'] = voxel_size
trackvis_header['dim'] = shape
trackvis_header['voxel_order'] = "RAS"
# Move streamlines to "trackvis space"
trackvis_point_space = utils.affine_for_trackvis(voxel_size)
lr_sf_trk = utils.move_streamlines(lr_superiorfrontal_track,
trackvis_point_space, input_space=affine)
lr_sf_trk = list(lr_sf_trk)
# Save streamlines
for_save = [(sl, None, None) for sl in lr_sf_trk]
nib.trackvis.write("lr-superiorfrontal.trk", for_save, trackvis_header)
"""
Let's take a moment here to consider the representation of streamlines used in
dipy. Streamlines are a path though the 3d space of an image represented by a
set of points. For these points to have a meaningful interpretation, these
points must be given in a known coordinate system. The ``affine`` attribute of
the ``streamline_generator`` object specifies the coordinate system of the
points with respect to the voxel indices of the input data.
def compute_correlation(data, distance, prototype_policies, num_prototypes, iterations, verbose=False, size_limit=1000):
global tracks_t,ids_l,data_original,tracks_s,id_t,tracks_n,a_ind, tracks_subsample
print "Computing distance matrix and similarity matrix (original space):",
data_original = data
if data.shape[0] > size_limit:
print
print "Datset too big: subsampling to %s entries only!" % size_limit
data = data[np.random.permutation(data.shape[0])[:size_limit], :]
od = distance(data, data)
print od.shape
original_distances = squareform(od)
#original_distances2 = squareform(od)
"""
my code
"""
affine=utils.affine_for_trackvis(voxel_size=np.array([2,2,2]))
lengths = list(length(data_original))
lengths=np.array(lengths)
temp=np.where(lengths>10)[0]
l=np.argsort(lengths)[::-1][:len(temp)]
data_original_temp=data_original[l]
a= streamline_mapping_new_step(data_original_temp, affine=affine)
tracks_subsample=data_original_temp[a]
print len(tracks_subsample)
"""
my code
"""
rho = np.zeros((len(prototype_policies), len(num_prototypes),iterations))
for m, prototype_policy in enumerate(prototype_policies):
print prototype_policy
for j, num_proto in enumerate(num_prototypes):
print "number of prototypes:", num_proto, " - ",
for k in range(iterations):
print k,
stdout.flush()
if verbose: print("Generating %s prototypes as" % num_proto),
# Note that we use the original dataset here, not the subsampled one!
if prototype_policy=='random':
if verbose: print("random subset of the initial data.")
prototype_idx = np.random.permutation(data_original.shape[0])[:num_proto]
prototype = [data_original[i] for i in prototype_idx]
elif prototype_policy=='sff':
prototype_idx = subset_furthest_first(data_original, num_proto, distance)
prototype = [data_original[i] for i in prototype_idx]
elif prototype_policy=='fft':
prototype_idx = furthest_first_traversal( tracks_subsample, num_proto, distance)
prototype = [ tracks_subsample[i] for i in prototype_idx]
else:
raise Exception
if verbose: print("Computing dissimilarity matrix.")
data_dissimilarity = distance(data, prototype)
if verbose: print("Computing distance matrix (dissimilarity space).")
dissimilarity_distances = pdist(data_dissimilarity, metric='euclidean')
rho[m,j,k] = correlation(original_distances, dissimilarity_distances)[0]
print
return rho
def compute_correlation(data,
distance,
prototype_policies,
num_prototypes,
iterations,
verbose=False,
size_limit=1000):
global tracks_t, ids_l, data_original, tracks_s, id_t, tracks_n, a_ind, tracks_subsample
print "Computing distance matrix and similarity matrix (original space):",
data_original = data
if data.shape[0] > size_limit:
print
print "Datset too big: subsampling to %s entries only!" % size_limit
data = data[np.random.permutation(data.shape[0])[:size_limit], :]
od = distance(data, data)
print od.shape
original_distances = squareform(od)
#original_distances2 = squareform(od)
"""
my code
"""
affine = utils.affine_for_trackvis(voxel_size=np.array([2, 2, 2]))
lengths = list(length(data_original))
lengths = np.array(lengths)
temp = np.where(lengths > 10)[0]
l = np.argsort(lengths)[::-1][:len(temp)]
data_original_temp = data_original[l]
a = streamline_mapping_new_step(data_original_temp, affine=affine)
tracks_subsample = data_original_temp[a]
print len(tracks_subsample)
"""
my code
"""
rho = np.zeros((len(prototype_policies), len(num_prototypes), iterations))
for m, prototype_policy in enumerate(prototype_policies):
print prototype_policy
for j, num_proto in enumerate(num_prototypes):
print "number of prototypes:", num_proto, " - ",
for k in range(iterations):
print k,
stdout.flush()
if verbose: print("Generating %s prototypes as" % num_proto),
# Note that we use the original dataset here, not the subsampled one!
if prototype_policy == 'random':
if verbose: print("random subset of the initial data.")
prototype_idx = np.random.permutation(
data_original.shape[0])[:num_proto]
prototype = [data_original[i] for i in prototype_idx]
elif prototype_policy == 'sff':
prototype_idx = subset_furthest_first(
data_original, num_proto, distance)
prototype = [data_original[i] for i in prototype_idx]
elif prototype_policy == 'fft':
prototype_idx = furthest_first_traversal(
tracks_subsample, num_proto, distance)
prototype = [tracks_subsample[i] for i in prototype_idx]
else:
raise Exception
if verbose: print("Computing dissimilarity matrix.")
data_dissimilarity = distance(data, prototype)
if verbose:
print("Computing distance matrix (dissimilarity space).")
dissimilarity_distances = pdist(data_dissimilarity,
metric='euclidean')
rho[m, j, k] = correlation(original_distances,
dissimilarity_distances)[0]
print
return rho
import numpy as np
import nibabel as nib
from dipy.tracking import utils
from dipy.tracking.utils import length
from mapping_test import *
"""
Reading the track
"""
streams1,hdr1=nib.trackvis.read('/home/nusrat/dataset_trackvis/101.trk')
tracks = np.array([s[0] for s in streams1], dtype=np.object)
"""
affine for converting the streamline cordinate with the voxel cordinate
"""
affine=utils.affine_for_trackvis(voxel_size=np.array([2,2,2]))
"""
length function from the dipy
https://github.com/nipy/dipy/blob/master/dipy/tracking/_utils.py
"""
lengths = list(length(tracks))
"""
fiter the whole tractography--like we are not interested the track less than 10.
"""
lengths=np.array(lengths)
l=np.where(lengths>10)[0]
"""
rearrange the tracktography
"""
def label_streamlines_density(streamlines,labels,affine,f_name,img,label_img):
"""
.. figure:: connectivity.png
:align: center
**Connectivity of Corpus Callosum**
.. include:: ../links_names.inc
"""
shape = labels.shape
dm = utils.density_map(streamlines, shape, affine=affine)
sum=0 ;count=0
for i in dm:
for j in i:
for k in j:
if (k != 0):
sum=sum+k
count += 1
density = sum*1.0/count
print density
"""
To do that, we will use tools available in [nibabel](http://nipy.org/nibabel)
"""
# Save density map
dm_img = nib.Nifti1Image(dm.astype("int16"), img.get_affine())
dm_img.to_filename(f_name+"-dm.nii.gz")
# Make a trackvis header so we can save streamlines
voxel_size = label_img.get_header().get_zooms()
trackvis_header = nib.trackvis.empty_header()
trackvis_header['voxel_size'] = voxel_size
trackvis_header['dim'] = shape
trackvis_header['voxel_order'] = "RAS"
# Move streamlines to "trackvis space"
trackvis_point_space = utils.affine_for_trackvis(voxel_size)
lr_sf_trk = utils.move_streamlines(streamlines,
trackvis_point_space, input_space=affine)
lr_sf_trk = list(lr_sf_trk)
"""
# Save streamlines
for_save = [(sl, None, None) for sl in lr_sf_trk]
nib.trackvis.write(f_name+"_label1.trk", for_save, trackvis_header)
"""
"""
import tractconverter as tc
density_file = f_name+"_label1.trk"
input_format=tc.detect_format(density_file)
input=input_format(density_file)
output=tc.FORMATS['vtk'].create(density_file+".vtk",input.hdr)
tc.convert(input,output)
"""
"""
Let's take a moment here to consider the representation of streamlines used in
dipy. Streamlines are a path though the 3d space of an image represented by a
set of points. For these points to have a meaningful interpretation, these
points must be given in a known coordinate system. The ``affine`` attribute of
the ``streamline_generator`` object specifies the coordinate system of the
points with respect to the voxel indices of the input data.
``trackvis_point_space`` specifies the trackvis coordinate system with respect
to the same indices. The ``move_streamlines`` function returns a new set of
streamlines from an existing set of streamlines in the target space. The
target space and the input space must be specified as affine transformations
with respect to the same reference [#]_. If no input space is given, the input
space will be the same as the current representation of the streamlines, in
other words the input space is assumed to be ``np.eye(4)``, the 4-by-4 identity
matrix.
All of the functions above that allow streamlines to interact with volumes take
an affine argument. This argument allows these functions to work with
streamlines regardless of their coordinate system. For example even though we
moved our streamlines to "trackvis space", we can still compute the density map
as long as we specify the right coordinate system.
"""
dm_trackvis = utils.density_map(lr_sf_trk, shape, affine=trackvis_point_space)
assert np.all(dm == dm_trackvis)
return dm,density
"""
This means that streamlines can interact with any image volume, for example a
high resolution structural image, as long as one can register that image to
the diffusion images and calculate the coordinate system with respect to that
image.
"""
"""
