def loadColourMapFile(fname, aslut=False):
"""Load the given file, assumed to be a colour map.
:arg fname: FSLeyes or FSLView (VEST) colour map file
:arg aslut: If ``True``, the returned array will contain a label for
each colour, ranging from ``1`` to ``N``, where ``N`` is
the number of colours in the file.
:returns: A ``numpy`` array of shape ``(N, 3)`` containing the
RGB values for ``N`` colours. Or, if ``aslut is True``,
A ``numpy`` array of shape ``(N, 4)`` containing a
label, and the RGB values for ``N`` colours.
"""
# The file could be a FSLView style VEST LUT
if vest.looksLikeVestLutFile(fname):
data = vest.loadVestLutFile(fname, normalise=False)
# Or just a plain 2D text array
else:
data = np.loadtxt(fname)
if aslut:
lbls = np.arange(1, data.shape[0] + 1).reshape(-1, 1)
data = np.hstack((lbls, data))
return data
def test_loadVestLutFile():
testdir = tempfile.mkdtemp()
testfiles = [
op.join(testdir, 'testfile1.txt'),
op.join(testdir, 'testfile2.txt'),
op.join(testdir, 'testfile3.txt'),
op.join(testdir, 'testfile4.txt'),
op.join(testdir, 'testfile5.txt')]
testdata = [
testfile1Colours,
testfile2Colours,
testfile3Colours,
testfile4Colours]
try:
_createFiles(testdir)
with pytest.raises(Exception):
vest.loadVestLutFile(testfiles[4])
vest.loadVestLutFile(testfiles[4], normalise=False)
for i in range(4):
f = testfiles[i]
d = testdata[ i]
with warnings.catch_warnings():
warnings.simplefilter('ignore')
dnorm = (d - d.min()) / (d.max() - d.min())
lutnorm = vest.loadVestLutFile(f)
lut = vest.loadVestLutFile(f, normalise=False)
assert lut.shape == d.shape
assert lutnorm.shape == dnorm.shape
assert np.all(np.isclose(lut, d))
if (d.max() - d.min()) != 0:
assert np.all(np.isclose(lutnorm, dnorm))
else:
assert np.all(np.isnan(dnorm))
assert np.all(np.isnan(lutnorm))
finally:
shutil.rmtree(testdir)
def registerColourMap(cmapFile,
overlayList=None,
displayCtx=None,
key=None,
name=None):
"""Loads RGB data from the given file, and registers
it as a :mod:`matplotlib` :class:`~matplotlib.colors.ListedColormap`
instance.
.. note:: If the ``overlayList`` and ``displayContext`` arguments are
provided, the ``cmap`` property of all :class:`.VolumeOpts`
instances are updated to support the new colour map.
:arg cmapFile: Name of a file containing RGB values
:arg overlayList: A :class:`.OverlayList` instance which contains all
overlays that are being displayed (can be ``None``).
:arg displayCtx: A :class:`.DisplayContext` instance describing how
the overlays in ``overlayList`` are being displayed.
Must be provided if ``overlayList`` is provided.
:arg key: Name to give the colour map. If ``None``, defaults
to the file name prefix.
:arg name: Display name for the colour map. If ``None``, defaults
to the ``name``.
"""
import matplotlib.cm as mplcm
import matplotlib.colors as colors
if key is not None and not isValidMapKey(key):
raise ValueError('{} is not a valid colour map identifier'.format(key))
if key is None:
key = op.basename(cmapFile).split('.')[0]
key = makeValidMapKey(key)
if name is None: name = key
if overlayList is None: overlayList = []
# The file could be a FSLView style VEST-LUT
if vest.looksLikeVestLutFile(cmapFile):
data = vest.loadVestLutFile(cmapFile, normalise=False)
# Or just a plain 2D text array
else:
data = np.loadtxt(cmapFile)
cmap = colors.ListedColormap(data, key)
log.debug('Loading and registering custom '
'colour map: {}'.format(cmapFile))
mplcm.register_cmap(key, cmap)
_cmaps[key] = _Map(key, name, cmap, cmapFile, False)
log.debug('Patching DisplayOpts instances and class '
'to support new colour map {}'.format(key))
import fsleyes.displaycontext as fsldisplay
# A list of all DisplayOpts colour map properties.
# n.b. We can't simply list the ColourMapOpts class
# here, because it is a mixin, and does not actually
# derive from props.HasProperties.
#
# TODO Any new DisplayOpts sub-types which have a
# colour map will need to be patched here
cmapProps = []
cmapProps.append((fsldisplay.VolumeOpts, 'cmap'))
cmapProps.append((fsldisplay.VolumeOpts, 'negativeCmap'))
cmapProps.append((fsldisplay.VectorOpts, 'cmap'))
cmapProps.append((fsldisplay.MeshOpts, 'cmap'))
cmapProps.append((fsldisplay.MeshOpts, 'negativeCmap'))
# Update the colour map properties
# for any existing instances
for overlay in overlayList:
opts = displayCtx.getOpts(overlay)
for cls, propName in cmapProps:
if isinstance(opts, cls):
prop = opts.getProp(propName)
prop.addColourMap(key, opts)
# and for all future overlays
for cls, propName in cmapProps:
prop = cls.getProp(propName)
prop.addColourMap(key)