Here we present an example for visualizing slices from 3D images. Let’s download and load a T1. Create a Scene object which holds all the actors which we want to visualize. The T1 has usually a higher range of values than what can be visualized in an
image. We can set the range that we would like to see. The The The same actor can show any different slice from the given data using its
Now we have a new In order to interact with the data you will need to uncomment the line below. Otherwise, you can save a screenshot using the following command. It is also possible to set the colormap of your preference. Here we are loading
an FA image and showing it in a non-standard way using an HSV colormap. This is because the lookup table is applied in the slice after interpolating
to (0, 255). Now we would like to add the ability to click on a voxel and show its value
on a panel in the window. The panel is a UI element which requires access to
different areas of the visualization pipeline and therefore we don’t recommend
using it with We’ll start by creating the panel and adding it to the Add a left-click callback to the slicer. Also disable interpolation so you can
see what you are picking. By using the So, let’s clear the scene and change the projection from perspective to
parallel. We’ll also need a new show manager and an associated callback. Now we need to create two nested for loops which will set the positions of
the grid of the mosaic and add the new actors to the scene. We are going
to use 15 columns and 10 rows but you can adjust those with your datasets. If you uncomment the two lines above, you will be able to move
the mosaic up/down and left/right using the middle mouse button drag,
zoom in/out using the scroll wheel, and pick voxels with left click. Example source code You can download Simple volume slicing
import os
from dipy.data import fetch_bundles_2_subjects
from dipy.io.image import load_nifti, load_nifti_data
from dipy.viz import window, actor, ui
fetch_bundles_2_subjects()
fname_t1 = os.path.join(os.path.expanduser('~'), '.dipy',
'exp_bundles_and_maps', 'bundles_2_subjects',
'subj_1', 't1_warped.nii.gz')
data, affine = load_nifti(fname_t1)
scene = window.Scene()
scene.background((0.5, 0.5, 0.5))
Render slices from T1 with a specific value range
mean, std = data[data > 0].mean(), data[data > 0].std()
value_range = (mean - 0.5 * std, mean + 1.5 * std)
slice
function will read data and resample the data using an affine
transformation matrix. The default behavior of this function is to show the
middle slice of the last dimension of the resampled data.slice_actor = actor.slicer(data, affine, value_range)
slice_actor
contains an axial slice.scene.add(slice_actor)
display
function. However, if we want to show multiple slices we need to
copy the actor first.slice_actor2 = slice_actor.copy()
slice_actor
which displays the middle slice of the
sagittal plane.slice_actor2.display(slice_actor2.shape[0]//2, None, None)
scene.add(slice_actor2)
scene.reset_camera()
scene.zoom(1.4)
# window.show(scene, size=(600, 600), reset_camera=False)
window.record(scene, out_path='slices.png', size=(600, 600),
reset_camera=False)
Render slices from FA with your colormap
fname_fa = os.path.join(os.path.expanduser('~'), '.dipy',
'exp_bundles_and_maps', 'bundles_2_subjects',
'subj_1', 'fa_1x1x1.nii.gz')
fa = load_nifti_data(fname_fa)
lut = actor.colormap_lookup_table(scale_range=(fa.min(), fa.max()*0.8),
hue_range=(0.4, 1.),
saturation_range=(1, 1.),
value_range=(0., 1.))
fa_actor = actor.slicer(fa, affine, lookup_colormap=lut)
scene.clear()
scene.add(fa_actor)
scene.reset_camera()
scene.zoom(1.4)
# window.show(scene, size=(600, 600), reset_camera=False)
window.record(scene, out_path='slices_lut.png', size=(600, 600),
reset_camera=False)
window.show
. The more appropriate way is to use the
ShowManager
object, which allows accessing the pipeline in different areas.show_m = window.ShowManager(scene, size=(1200, 900))
show_m.initialize()
ShowManager
label_position = ui.TextBlock2D(text='Position:')
label_value = ui.TextBlock2D(text='Value:')
result_position = ui.TextBlock2D(text='')
result_value = ui.TextBlock2D(text='')
panel_picking = ui.Panel2D(size=(250, 125),
position=(20, 20),
color=(0, 0, 0),
opacity=0.75,
align="left")
panel_picking.add_element(label_position, (0.1, 0.55))
panel_picking.add_element(label_value, (0.1, 0.25))
panel_picking.add_element(result_position, (0.45, 0.55))
panel_picking.add_element(result_value, (0.45, 0.25))
scene.add(panel_picking)
def left_click_callback(obj, ev):
"""Get the value of the clicked voxel and show it in the panel."""
event_pos = show_m.iren.GetEventPosition()
obj.picker.Pick(event_pos[0], event_pos[1], 0, scene)
i, j, k = obj.picker.GetPointIJK()
result_position.message = '({}, {}, {})'.format(str(i), str(j), str(k))
result_value.message = '%.8f' % data[i, j, k]
fa_actor.SetInterpolate(False)
fa_actor.AddObserver('LeftButtonPressEvent', left_click_callback, 1.0)
# show_m.start()
Create a mosaic
copy
and display
method of the slice_actor
it becomes
easy and efficient to create a mosaic of all the slices.scene.clear()
scene.projection('parallel')
result_position.message = ''
result_value.message = ''
show_m_mosaic = window.ShowManager(scene, size=(1200, 900))
show_m_mosaic.initialize()
def left_click_callback_mosaic(obj, ev):
"""Get the value of the clicked voxel and show it in the panel."""
event_pos = show_m_mosaic.iren.GetEventPosition()
obj.picker.Pick(event_pos[0], event_pos[1], 0, scene)
i, j, k = obj.picker.GetPointIJK()
result_position.message = '({}, {}, {})'.format(str(i), str(j), str(k))
result_value.message = '%.8f' % data[i, j, k]
cnt = 0
X, Y, Z = slice_actor.shape[:3]
rows = 10
cols = 15
border = 10
for j in range(rows):
for i in range(cols):
slice_mosaic = slice_actor.copy()
slice_mosaic.display(None, None, cnt)
slice_mosaic.SetPosition((X + border) * i,
0.5 * cols * (Y + border) - (Y + border) * j,
0)
slice_mosaic.SetInterpolate(False)
slice_mosaic.AddObserver('LeftButtonPressEvent',
left_click_callback_mosaic,
1.0)
scene.add(slice_mosaic)
cnt += 1
if cnt > Z:
break
if cnt > Z:
break
scene.reset_camera()
scene.zoom(1.0)
# show_m_mosaic.ren.add(panel_picking)
# show_m_mosaic.start()
window.record(scene, out_path='mosaic.png', size=(900, 600),
reset_camera=False)
the full source code of this example
. This same script is also included in the dipy source distribution under the doc/examples/
directory.