.. 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_viz_slice.py: ===================== Simple volume slicing ===================== Here we present an example for visualizing slices from 3D images. .. code-block:: python from __future__ import division 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:: python 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 .. rst-class:: sphx-glr-script-out Out: .. code-block:: none Data size is approximately 234MB Dataset is already in place. If you want to fetch it again please first remove the folder /Users/koudoro/.dipy/exp_bundles_and_maps Create a Renderer object which holds all the actors which we want to visualize. .. code-block:: python renderer = window.Renderer() renderer.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:: python 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:: python slice_actor = actor.slicer(data, affine, value_range) The ``slice_actor`` contains an axial slice. .. code-block:: python renderer.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:: python slice_actor2 = slice_actor.copy() Now we have a new ``slice_actor`` which displays the middle slice of sagittal plane. .. code-block:: python slice_actor2.display(slice_actor2.shape[0]//2, None, None) renderer.add(slice_actor2) renderer.reset_camera() renderer.zoom(1.4) In order to interact with the data you will need to uncomment the line below. .. code-block:: python # window.show(renderer, size=(600, 600), reset_camera=False) Otherwise, you can save a screenshot using the following command. .. code-block:: python window.record(renderer, out_path='slices.png', size=(600, 600), reset_camera=False) .. image:: /auto_tutorials/images/sphx_glr_viz_slice_001.png :class: sphx-glr-single-img Render slices from FA with your colormap ======================================== .. code-block:: python # 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 (0, 255) and not (0, 1) which is the usual range of FA values. .. code-block:: python lut = actor.colormap_lookup_table(scale_range=(0, 255), 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:: python fa_actor = actor.slicer(fa, affine, lookup_colormap=lut) renderer.clear() renderer.add(fa_actor) renderer.reset_camera() renderer.zoom(1.4) # window.show(renderer, size=(600, 600), reset_camera=False) window.record(renderer, out_path='slices_lut.png', size=(600, 600), reset_camera=False) .. image:: /auto_tutorials/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:: python show_m = window.ShowManager(renderer, size=(1200, 900)) show_m.initialize() We'll start by creating the panel and adding it to the ``ShowManager`` .. code-block:: python 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.ren.add(panel_picking) Add a left-click callback to the slicer. Also disable interpolation so you can see what you are picking. .. code-block:: python 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.ren) 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 renderer and change the projection from perspective to parallel. We'll also need a new show manager and an associated callback. .. code-block:: python renderer.clear() renderer.projection('parallel') result_position.message = '' result_value.message = '' show_m_mosaic = window.ShowManager(renderer, 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.ren) 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 renderer. We are going to use 15 columns and 10 rows but you can adjust those with your datasets. .. code-block:: python 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) renderer.add(slice_mosaic) cnt += 1 if cnt > Z: break if cnt > Z: break renderer.reset_camera() renderer.zoom(1.0) # show_m_mosaic.ren.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:: python window.record(renderer, out_path='mosaic.png', size=(900, 600), reset_camera=False) .. image:: /auto_tutorials/images/sphx_glr_viz_slice_003.png :class: sphx-glr-single-img **Total running time of the script:** ( 0 minutes 4.268 seconds) .. _sphx_glr_download_auto_tutorials_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 `_