Merge pull request #404 from Eric89GXL/pauls-viewer

MRG: Slice viewer

Orthogonal slice viewer for 3D and 4D images.  Based on Paul Ivanov's prototype.   Viewers can be yoked so that crosshairs correspond to matching voxel coordinates according to the image affines.

Author: matthew-brett

.travis.yml

@@ -3,6 +3,7 @@
 # munges each line before executing it to print out the exit status.  It's okay
 # for it to be on multiple physical lines, so long as you remember: - There
 # can't be any leading "-"s - All newlines will be removed, so use ";"s
+
 language: python
 
 # Run jobs on container-based infrastructure, can be overridden per job

nibabel/__init__.py

@@ -64,6 +64,7 @@
 from .imageclasses import class_map, ext_map, all_image_classes
 from . import trackvis
 from . import mriutils
+from . import viewers
 
 # be friendly on systems with ancient numpy -- no tests, but at least
 # importable

nibabel/spatialimages.py

@@ -139,6 +139,7 @@
 
 from .filebasedimages import FileBasedHeader, FileBasedImage
 from .filebasedimages import ImageFileError  # flake8: noqa; for back-compat
+from .viewers import OrthoSlicer3D
 from .volumeutils import shape_zoom_affine
 
 
@@ -661,3 +662,20 @@ def __getitem__(self):
         raise TypeError("Cannot slice image objects; consider slicing image "
                         "array data with `img.dataobj[slice]` or "
                         "`img.get_data()[slice]`")
+
+    def orthoview(self):
+        """Plot the image using OrthoSlicer3D
+
+        Returns
+        -------
+        viewer : instance of OrthoSlicer3D
+            The viewer.
+
+        Notes
+        -----
+        This requires matplotlib. If a non-interactive backend is used,
+        consider using viewer.show() (equivalently plt.show()) to show
+        the figure.
+        """
+        return OrthoSlicer3D(self.dataobj, self.affine,
+                             title=self.get_filename())

nibabel/tests/test_viewers.py

@@ -0,0 +1,94 @@
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+
+import numpy as np
+from collections import namedtuple as nt
+
+
+from ..optpkg import optional_package
+from ..viewers import OrthoSlicer3D
+
+from numpy.testing.decorators import skipif
+from numpy.testing import assert_array_equal, assert_equal
+
+from nose.tools import assert_raises, assert_true
+
+matplotlib, has_mpl = optional_package('matplotlib')[:2]
+needs_mpl = skipif(not has_mpl, 'These tests need matplotlib')
+if has_mpl:
+    matplotlib.use('Agg')
+
+
+@needs_mpl
+def test_viewer():
+    # Test viewer
+    plt = optional_package('matplotlib.pyplot')[0]
+    a = np.sin(np.linspace(0, np.pi, 20))
+    b = np.sin(np.linspace(0, np.pi*5, 30))
+    data = (np.outer(a, b)[..., np.newaxis] * a)[:, :, :, np.newaxis]
+    data = data * np.array([1., 2.])  # give it a # of volumes > 1
+    v = OrthoSlicer3D(data)
+    assert_array_equal(v.position, (0, 0, 0))
+    assert_true('OrthoSlicer3D' in repr(v))
+
+    # fake some events, inside and outside axes
+    v._on_scroll(nt('event', 'button inaxes key')('up', None, None))
+    for ax in (v._axes[0], v._axes[3]):
+        v._on_scroll(nt('event', 'button inaxes key')('up', ax, None))
+    v._on_scroll(nt('event', 'button inaxes key')('up', ax, 'shift'))
+    # "click" outside axes, then once in each axis, then move without click
+    v._on_mouse(nt('event', 'xdata ydata inaxes button')(0.5, 0.5, None, 1))
+    for ax in v._axes:
+        v._on_mouse(nt('event', 'xdata ydata inaxes button')(0.5, 0.5, ax, 1))
+    v._on_mouse(nt('event', 'xdata ydata inaxes button')(0.5, 0.5, None, None))
+    v.set_volume_idx(1)
+    v.cmap = 'hot'
+    v.clim = (0, 3)
+    assert_raises(ValueError, OrthoSlicer3D.clim.fset, v, (0.,))  # bad limits
+    assert_raises(ValueError, OrthoSlicer3D.cmap.fset, v, 'foo')  # wrong cmap
+
+    # decrement/increment volume numbers via keypress
+    v.set_volume_idx(1)  # should just pass
+    v._on_keypress(nt('event', 'key')('-'))  # decrement
+    assert_equal(v._data_idx[3], 0)
+    v._on_keypress(nt('event', 'key')('+'))  # increment
+    assert_equal(v._data_idx[3], 1)
+    v._on_keypress(nt('event', 'key')('-'))
+    v._on_keypress(nt('event', 'key')('='))  # alternative increment key
+    assert_equal(v._data_idx[3], 1)
+
+    v.close()
+    v._draw()  # should be safe
+
+    # non-multi-volume
+    v = OrthoSlicer3D(data[:, :, :, 0])
+    v._on_scroll(nt('event', 'button inaxes key')('up', v._axes[0], 'shift'))
+    v._on_keypress(nt('event', 'key')('escape'))
+    v.close()
+
+    # complex input should raise a TypeError prior to figure creation
+    assert_raises(TypeError, OrthoSlicer3D,
+                  data[:, :, :, 0].astype(np.complex64))
+
+    # other cases
+    fig, axes = plt.subplots(1, 4)
+    plt.close(fig)
+    v1 = OrthoSlicer3D(data, axes=axes)
+    aff = np.array([[0, 1, 0, 3], [-1, 0, 0, 2], [0, 0, 2, 1], [0, 0, 0, 1]],
+                   float)
+    v2 = OrthoSlicer3D(data, affine=aff, axes=axes[:3])
+    # bad data (not 3+ dim)
+    assert_raises(ValueError, OrthoSlicer3D, data[:, :, 0, 0])
+    # bad affine (not 4x4)
+    assert_raises(ValueError, OrthoSlicer3D, data, affine=np.eye(3))
+    assert_raises(TypeError, v2.link_to, 1)
+    v2.link_to(v1)
+    v2.link_to(v1)  # shouldn't do anything
+    v1.close()
+    v2.close()