MRG: Slice viewer

.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()