.. note:: :class: sphx-glr-download-link-note Click :ref:`here ` to download the full example code .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_tutorials_01_introductory_viz_slice.py: ===================== Simple volume slicing ===================== Here we present an example for visualizing slices from 3D images. .. code-block:: default import os import nibabel as nib from dipy.data import fetch_bundles_2_subjects from fury import window, actor, ui Let's download and load a T1. .. code-block:: default 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') img = nib.load(fname_t1) data = img.get_data() affine = img.affine Create a Scene object which holds all the actors which we want to visualize. .. code-block:: default scene = window.Scene() scene.background((0.5, 0.5, 0.5)) Render slices from T1 with a specific value range ================================================= 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. .. code-block:: default mean, std = data[data > 0].mean(), data[data > 0].std() value_range = (mean - 0.5 * std, mean + 1.5 * std) The ``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. .. code-block:: default slice_actor = actor.slicer(data, affine, value_range) The ``slice_actor`` contains an axial slice. .. code-block:: default scene.add(slice_actor) The same actor can show any different slice from the given data using its ``display`` function. However, if we want to show multiple slices we need to copy the actor first. .. code-block:: default slice_actor2 = slice_actor.copy() Now we have a new ``slice_actor`` which displays the middle slice of sagittal plane. .. code-block:: default slice_actor2.display(slice_actor2.shape[0]//2, None, None) scene.add(slice_actor2) scene.reset_camera() scene.zoom(1.4) In order to interact with the data you will need to uncomment the line below. .. code-block:: default # window.show(scene, size=(600, 600), reset_camera=False) Otherwise, you can save a screenshot using the following command. .. code-block:: default window.record(scene, out_path='slices.png', size=(600, 600), reset_camera=False) .. image:: /auto_tutorials/01_introductory/images/sphx_glr_viz_slice_001.png :class: sphx-glr-single-img Render slices from FA with your colormap ======================================== .. code-block:: default # 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. fname_fa = os.path.join(os.path.expanduser('~'), '.dipy', 'exp_bundles_and_maps', 'bundles_2_subjects', 'subj_1', 'fa_1x1x1.nii.gz') img = nib.load(fname_fa) fa = img.get_data() Notice here how the scale range is. We use FA min and max values to set it up .. code-block:: default lut = actor.colormap_lookup_table(scale_range=(fa.min(), fa.max()), hue_range=(0.4, 1.), saturation_range=(1, 1.), value_range=(0., 1.)) This is because the lookup table is applied in the slice after interpolating to (0, 255). .. code-block:: default 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) .. image:: /auto_tutorials/01_introductory/images/sphx_glr_viz_slice_002.png :class: sphx-glr-single-img 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 ``window.show``. The more appropriate way is to use the ``ShowManager`` object, which allows accessing the pipeline in different areas. .. code-block:: default show_m = window.ShowManager(scene, size=(1200, 900)) show_m.initialize() We'll start by creating the panel and adding it to the ``ShowManager`` .. code-block:: default 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)) show_m.scene.add(panel_picking) Add a left-click callback to the slicer. Also disable interpolation so you can see what you are picking. .. code-block:: default 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, show_m.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 ================ By using the ``copy`` and ``display`` method of the ``slice_actor`` becomes easy and efficient to create a mosaic of all the slices. 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. .. code-block:: default 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, show_m_mosaic.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] 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. .. code-block:: default 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.scene.add(panel_picking) # show_m_mosaic.start() 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. .. code-block:: default window.record(scene, out_path='mosaic.png', size=(900, 600), reset_camera=False) .. image:: /auto_tutorials/01_introductory/images/sphx_glr_viz_slice_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 4.285 seconds) .. _sphx_glr_download_auto_tutorials_01_introductory_viz_slice.py: .. only :: html .. container:: sphx-glr-footer :class: sphx-glr-footer-example .. container:: sphx-glr-download :download:`Download Python source code: viz_slice.py ` .. container:: sphx-glr-download :download:`Download Jupyter notebook: viz_slice.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_