def DispImage(im, title=None,
sliceIdx=None, dim='z',
cmap='gray', newFig=True,
rng=None, t=False, log=False):
# if this volume is not a slice already, extract a slice
sz = im.size().tolist()
if sz[common.DIMMAP[dim]] > 1:
im = common.ExtractSliceIm(im, sliceIdx, dim)
im.toType(core.MEM_HOST)
# transfer to host memory if necessary
if im.memType() == core.MEM_DEVICE:
tmp = core.Image3D(im.grid(), core.MEM_HOST)
core.Copy(tmp, im)
im = tmp
# create the figure if requested
if newFig:
if title is None:
plt.figure()
else:
plt.figure(title)
plt.clf()
# set the range
if rng is None:
vmin = None
vmax = None
else:
vmin = rng[0]
vmax = rng[1]
if log:
norm = matplotlib.colors.LogNorm(vmin=vmin, vmax=vmax)
else:
norm = matplotlib.colors.Normalize(vmin=vmin, vmax=vmax)
# convert to numpy array
arr = np.squeeze(im.asnp().copy())
# transpose if requested
if t:
arr = arr.T
# display
plt.imshow(arr, cmap=cmap, vmin=vmin, vmax=vmax, norm=norm, interpolation='nearest')
plt.axis('tight')
plt.axis('image')
if title is not None:
plt.title(title)
plt.xticks([])
plt.yticks([])
plt.draw()
def SaveSlice(fname, im, sliceIdx=None, dim='z',
cmap='gray', rng=None, t=True):
sliceIm = common.ExtractSliceIm(im, sliceIdx, dim)
sliceIm.toType(core.MEM_HOST)
if rng is None:
vmin = None
vmax = None
else:
vmin = rng[0]
vmax = rng[1]
if t:
plt.imsave(fname, np.squeeze(sliceIm.asnp()).T,
cmap=cmap, vmin=vmin, vmax=vmax)
else:
plt.imsave(fname, np.squeeze(sliceIm.asnp()),
cmap=cmap, vmin=vmin, vmax=vmax)
def ExtractSliceFunc(IDef, t):
sliceIm = common.ExtractSliceIm(IDef)
return sliceIm
BFI_color3D = cc.LoadMHA(dir_bf + 'block' + str(block) + '_reg_rgb.mha',
ca.MEM_HOST)
BFIDef3D_RGB = ca.Field3D(BFI3D.grid(), BFI3D.memType())
ca.SetMem(BFIDef3D_RGB, 0.0)
if SaveVE:
BFIDef3D_VE = ca.Image3D(BFI3D.grid(), BFI3D.memType())
ca.SetMem(BFIDef3D_VE, 0.0)
if SaveBW:
BFIDef3D_BW = ca.Image3D(BFI3D.grid(), BFI3D.memType())
ca.SetMem(BFIDef3D_BW, 0.0)
if SaveVF:
BFIDef3D_VF = ca.Image3D(BFI3D.grid(), BFI3D.memType())
ca.SetMem(BFIDef3D_VF, 0.0)
# Initialize the 2D slices
BFI = common.ExtractSliceIm(BFI3D, 0)
BFI.toType(ca.MEM_DEVICE)
BFI.setOrigin(ca.Vec3Df(0, 0, 0))
print BFI.grid()
grid2D = BFI.grid().copy()
if SaveRGB:
BFI_def_RGB = ca.Field3D(grid2D, BFI.memType())
ca.SetMem(BFI_def_RGB, 0.0)
if SaveVE:
BFI_def_VE = ca.Image3D(grid2D, BFI.memType())
ca.SetMem(BFI_def_VE, 0.0)
if SaveBW:
BFI_def_BW = ca.Image3D(grid2D, BFI.memType())
ca.SetMem(BFI_def_BW, 0.0)
for sliceIdx in xrange(BFI3D.grid().size().z):