NF: add version of Paul Ivanov's slice viewer

.gitignore

@@ -58,6 +58,7 @@ dist/
 .shelf
 .tox/
 .coverage
+cover/
 
 # Logs and databases #
 ######################

.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
 env:
     global:
@@ -44,7 +45,12 @@ before_install:
     - if [[ $DEPENDS == *h5py* ]]; then
       sudo apt-get install libhdf5-serial-dev;
       fi
-# command to install dependencies
+    # Create a (fake) display on Travis so that mpl tests work
+    # TODO: Could also use the `agg` backend instead
+    - if [[ $DEPENDS == "*matplotlib*" ]]; then
+      export DISPLAY=:99.0;
+      /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
+      fi;
 install:
     - python setup.py install
     # Point to nibabel data directory

nibabel/__init__.py

@@ -64,6 +64,7 @@
 from .imageclasses import class_map, ext_map
 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

@@ -143,6 +143,7 @@
 
 from .filename_parser import types_filenames, TypesFilenamesError
 from .fileholders import FileHolder
+from .viewers import OrthoSlicer3D
 from .volumeutils import shape_zoom_affine
 
 
@@ -744,3 +745,20 @@ def __getitem__(self):
         raise TypeError("Cannot slice image objects; consider slicing image "
                         "array data with `img.dataobj[slice]` or "
                         "`img.get_data()[slice]`")
+
+    def plot(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.get_data(), self.get_affine(),
+                             title=self.get_filename())

nibabel/tests/test_viewers.py

@@ -0,0 +1,73 @@
+# 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
+
+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.set_volume_idx(1)  # should just pass
+    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'))
+
+    # other cases
+    fig, axes = plt.subplots(1, 4)
+    plt.close(fig)
+    v1 = OrthoSlicer3D(data, pcnt_range=[0.1, 0.9], 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])
+    assert_raises(ValueError, OrthoSlicer3D, data[:, :, 0, 0])
+    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()