def __init__(self,
name,
vol=None,
hdr=None,
method='mip',
threshold=0.,
cmap='OpaqueGrays',
select=None,
transform=None,
parent=None,
preload=True,
verbose=None,
**kw):
"""Init."""
_Volume.__init__(self, name, parent, transform, verbose, **kw)
# _______________________ CHECKING _______________________
# Create 3-D volume :
vol_d = np.zeros((1, 1, 1), dtype=np.float32)
self._vol3d = visuals.Volume(vol_d,
parent=self._node,
threshold=threshold,
name='3-D Volume',
cmap=VOLUME_CMAPS[cmap])
if preload:
self(name, vol, hdr, threshold, cmap, method, select)
def __init__(self, parent=None, cmap='OpaqueGrays'):
"""Init."""
# Create the node for the 3-D volume :
self._node_vol = scene.Node(name='Volume3D')
self._node_vol.parent = parent
# Colormaps :
self._cmap_vol = cmap
self._cmaps = {}
self._cmaps['TransFire'] = TransFire()
self._cmaps['OpaqueFire'] = OpaqueFire()
self._cmaps['TransGrays'] = TransGrays()
self._cmaps['OpaqueGrays'] = OpaqueGrays()
# Create 3-D volume :
vol = np.zeros((1, 1, 1), dtype=np.float32)
self.vol3d = visu.Volume(vol,
parent=self._node_vol,
threshold=0.,
cmap=self._cmaps[cmap])
def show(self,clim=None,cmap = None):
# add a volume into the scene
# vol_data = np.load(io.load_data_file('brain/mri.npz'))['data']
# print type(vol_data)
# print vol_data.shape
# vol_data = np.flipud(np.rollaxis(vol_data, 1))
# print type(vol_data)
# print vol_data.shape
vol_data = self._pixel_array.copy()
# vol_data = np.gradient(self._pixel_array)
# vol_data = np.sqrt(vol_data[0] ** 2 + vol_data[1] ** 2 + vol_data[2] ** 2)
# print vol_data.shape
clim = clim or [-3024, 3071]
cmap = cmap or 'grays'
volume = visuals.Volume(vol_data, clim=clim,cmap = cmap,method = 'mip',relative_step_size=0.8,emulate_texture=False)
view.add(volume)
view.camera.set_range() # similar to viewAll in Coin3D