def test_iter_axes_masked():
arr = seq_array((5,4,3,2))
a = np.ma.array(arr, mask=(arr % 2 == 0))
b = list(iter_axes(a, 3))
# All even numbers are masked
assert_array_equal(a[:,:,:,0].mask, np.ones((5, 4, 3), dtype=bool))
assert_array_equal(a[:,:,:,1].mask, np.zeros((5, 4, 3), dtype=bool))
def test_iter_axes():
a = seq_array((5,4,3))
arrs = list(iter_axes(a, -1))
assert 3 == len(arrs)
assert_array_equal(a[...,0], arrs[0])
assert_array_equal(a[...,1], arrs[1])
assert_array_equal(a[...,2], arrs[2])
def test_iter_axes_multiple():
a = seq_array((5,4,3,2))
arrs = list(iter_axes(a, [2,3]))
assert 6 == len(arrs)
assert_array_equal(a[:,:,0,0], arrs[0])
assert_array_equal(a[:,:,0,1], arrs[1])
assert_array_equal(a[:,:,1,0], arrs[2])
assert_array_equal(a[:,:,1,1], arrs[3])
assert_array_equal(a[:,:,2,0], arrs[4])
assert_array_equal(a[:,:,2,1], arrs[5])
def test_iter_axes_none():
a = np.ones((5,4))
assert 0 == len(list(iter_axes(a, [])))
def view(dicoms, groupby=tuple(), roi_filename=None, roi_tag=None, viewer=None, viewer_kws=None):
"""Display a dicomset with arrview
Parameters
==========
dicoms : iterable of dicoms
An iterable of dicoms
groupby
Before displaying, group the dicoms (see data function)
roi_filename : str
Filename of rois to load. If not specified and the dicomset
has rois, then those are loaded instead.
roi_tag : str (default: '/')
When using the rois from the dicomset, this is the roi tag to load.
viewer : str
Either arrview or matplotlib.
viewer_kws : dict (default: {})
Keyword arguments to send to the viewer
Returns
=======
Displays the dicoms using arrview and returns the instance once
the window closes.
"""
viewer = viewer or 'arrview'
viewer_kws = viewer_kws or {}
arr = data(dicoms, field='pixel_array', groupby=groupby)
if viewer == 'matplotlib':
assert 2 <= arr.ndim <= 4, 'matplotlib viewer can only handle 4 or less dims'
import pylab
from matplotlib import gridspec
shape = arr.shape
nrows = 1 if arr.ndim < 3 else shape[2]
ncols = 1 if arr.ndim < 4 else shape[3]
figure_kws = viewer_kws.get('figure_kws', {})
if 'figsize' not in figure_kws:
aspect_ratio = ncols * shape[1] / float(nrows * shape[0])
height = 10
figure_kws['figsize'] = (height * aspect_ratio, height)
fig = pylab.figure(**figure_kws)
gs = gridspec.GridSpec(nrows, ncols, wspace=0, hspace=0)
first_ax = None
for spec, im in zip(iter(gs), iter_axes(arr, range(arr.ndim)[2:])):
ax = pylab.subplot(spec, sharex=first_ax, sharey=first_ax)
if first_ax is None:
first_ax = ax
ax.set_axis_off()
ax.set_aspect('equal')
ax.imshow(im, **viewer_kws.get('imshow_kws', {}))
return fig
elif viewer == 'arrview':
import arrview
dcm = dicoms.first
if roi_filename is None and dcm.meta.get('roi_filename'):
roi_filename = dcm.meta.roi_filename.get(roi_tag)
else:
roi_filename = os.path.dirname(dcm.filename)
return arrview.view(arr, roi_filename=roi_filename, **viewer_kws)
else:
raise Exception('Unknown viewer %r' % viewer)