1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427
|
Image Registration
==================
The :py:mod:`dtcwt.registration` module provides an implementation of a
DTCWT-based image registration algorithm. The output is similar, but not
identical, to "optical flow". The underlying assumption is that the source
image is a smooth locally-affine warping of a reference image. This assumption
is valid in some classes of medical image registration and for video sequences
with small motion between frames.
Algorithm overview
------------------
This section provides a brief overview of the algorithm itself. The algorithm
is a 2D version of the 3D registration algorithm presented in `Efficient
Registration of Nonrigid 3-D Bodies
<http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5936113&tag=1>`_. The
motion field between two images is a vector field whose elements represent the
direction and distance of displacement for each pixel in the source image
required to map it to a corresponding pixel in the reference image. In this
algorithm the motion is described via the affine transform which can represent
rotation, translation, shearing and scaling. An advantage of this model is that
if the motion of two neighbouring pixels are from the same model then they will
share affine transform parameters. This allows for large regions of the image
to be considered as a whole and helps mitigate the aperture problem.
The model described below is based on the model in `Phase-based
multidimensional volume registration
<http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1176641>`_ with changes
designed to allow use of the DTCWT as a front end.
Motion constraint
'''''''''''''''''
The three-element homogeneous displacement vector at location
:math:`\mathbf{x}` is defined to be
.. math::
\mathbf{\tilde{v}}(\mathbf{x}) \equiv \begin{bmatrix}
\mathbf{v}(\mathbf{x}) \\ 1
\end{bmatrix}
where :math:`\mathbf{v}(\mathbf{x})` is the motion vector at location
:math:`\mathbf{x} = [ x \, y ]^T`. A motion constraint is a three-element
vector, :math:`\mathbf{c}(\mathbf{x})` such that
.. math::
\mathbf{c}^T(\mathbf{x}) \, \mathbf{\tilde{v}}(\mathbf{x}) = 0.
In the two-dimensional DTCWT, the phase of each complex highpass coefficient
has an approximately linear relationship with the local shift vector. We can
therefore write
.. math::
\frac{\partial \theta_d}{\partial t} =
\nabla_\mathbf{x} \theta_d \cdot \mathbf{v}(\mathbf{x})
where :math:`\nabla_\mathbf{x} \theta_d \equiv [(\partial \theta_d/\partial
x) \, (\partial \theta_d/\partial y)]^T` and represents the phase gradient at
:math:`\mathbf{x}` for subband :math:`d` in both of the :math:`x` and :math:`y`
directions.
Numerical estimation of the partial derivatives of :math:`\theta_d` can be
performed by noting that multiplication of a subband pixels's complex
coefficient by the conjugate of its neighbour subtracts phase whereas
multiplication by the neighbour adds phase. We can thus construct equivalents
of forward-, backward- and central difference algorithms for phase gradients.
Comparing the relations above, it is clear that the motion constraint vector,
:math:`\mathbf{c}_d(\mathbf{x})`, corresponding to subband :math:`d` at location
:math:`\mathbf{x}` satisfies the following:
.. math::
\mathbf{c}_d(\mathbf{x}) = C_d(\mathbf{x}) \begin{bmatrix}
\nabla_\mathbf{x} \theta_d \\ - \frac{\partial \theta_d}{\partial t}
\end{bmatrix}
where :math:`C_d(\mathbf{x})` is some weighting factor which we can interpret
as a measure of the confidence we have of subband :math:`d` specifying the
motion at :math:`\mathbf{x}`.
This confidence measure can be heuristically designed. The measure used in this
implementation is:
.. math::
C_d(\mathbf{x}) = \frac{
\left| \sum_{k=1}^4 u_k^* v_k \right|^2
}{
\sum_{k=1}^4 (\left|u_k\right|^3 + \left|v_k\right|^3) + \epsilon
}.
where :math:`u_k` and :math:`v_k` are the wavelet coefficients in the reference
and source transformed images, subscripts :math:`k = 1 \dots 4` denote the four
diagonally neighbouring coefficients and :math:`\epsilon` is some small value
to avoid division by zero when the wavelet coefficients are small. It is beyond
the scope of this documentation to describe the design of this metric. Refer to
the `original paper
<http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5936113&tag=1>`_ for more
details.
Cost function
'''''''''''''
The model is represented via the six parameters :math:`a_1 \dots a_6` such that
.. math::
\mathbf{v}(\mathbf{x}) =
\begin{bmatrix}
1 & 0 & x & 0 & y & 0 \\
0 & 1 & 0 & x & 0 & y
\end{bmatrix}
\begin{bmatrix}
a_1 \\ \vdots \\ a_6
\end{bmatrix}
\equiv
\mathbf{K}(\mathbf{x}) \, \mathbf{a}.
We then make the following definitions:
.. math::
\mathbf{\tilde{K}}(\mathbf{x}) \equiv \begin{bmatrix}
\mathbf{K}(\mathbf{x}) & \mathbf{0} \\
\mathbf{0} & 1
\end{bmatrix},
\quad
\mathbf{\tilde{a}} \equiv \begin{bmatrix}
\mathbf{a} \\ 1
\end{bmatrix}
and then the homogenous motion vector is given by
.. math::
\mathbf{\tilde{v}}(\mathbf{x}) =
\mathbf{\tilde{K}}(\mathbf{x}) \, \mathbf{\tilde{a}}.
Considering all size subband directions, we have:
.. math::
\mathbf{c}_d(\mathbf{x}) \, \mathbf{\tilde{K}}(\mathbf{x}) \, \mathbf{\tilde{a}} = 0,
\quad \forall \ d \in \left\{ 1, \dots, 6 \right\}.
Each location :math:`\mathbf{x}` has six constraint equations for six unknown
affine parameters in :math:`\mathbf{\tilde{a}}`. We can solve for
:math:`\mathbf{\tilde{a}}` by minimising squared error
:math:`\epsilon(\mathbf{x})`:
.. math::
\begin{aligned}
\epsilon(\mathbf{x}) &= \sum_{d=1}^6 \left\|
\mathbf{c}_d^T(\mathbf{x}) \mathbf{\tilde{K}}(\mathbf{x}) \mathbf{\tilde{a}}
\right\|^2 \\
&= \sum_{d=1}^6
\mathbf{\tilde{a}}^T \, \mathbf{\tilde{K}}^T(\mathbf{x}) \, \mathbf{c}_d(\mathbf{x})
\mathbf{c}^T_d(\mathbf{x}) \, \mathbf{\tilde{K}}(\mathbf{x}) \, \mathbf{\tilde{a}} \\
&= \mathbf{\tilde{a}}^T \mathbf{\tilde{Q}}(\mathbf{x}) \mathbf{\tilde{a}}
\end{aligned}
where
.. math::
\mathbf{\tilde{Q}}(\mathbf{x}) \equiv \sum_{d=1}^6
\mathbf{\tilde{K}}^T(\mathbf{x}) \, \mathbf{c}_d(\mathbf{x})
\mathbf{c}^T_d(\mathbf{x}) \, \mathbf{\tilde{K}}(\mathbf{x}).
In practice, in order to handle the registration of dissimilar image features
and also to handle the aperture problem, it is helpful to combine
:math:`\mathbf{\tilde{Q}}(\mathbf{x})` matrices across more than one level of
DTCWT and over a slightly wider area within each level. This results in better
estimates of the affine parameters and reduces the likelihood of obtaining
singular matrices. We define locality :math:`\mathbf{\chi}` to represent this
wider spatial and inter-scale region, such that
.. math::
\mathbf{\tilde{Q}}_\mathbf{\chi} = \sum_{\mathbf{x} \in \mathbf{\chi}}
\mathbf{\tilde{Q}}(\mathbf{x}).
The :math:`\mathbf{\tilde{Q}}_\mathbf{\chi}` matrices are symmetric and so can
be written in the following form:
.. math::
\mathbf{\tilde{Q}}_\mathbf{\chi} = \begin{bmatrix}
\mathbf{Q}_\mathbf{\chi} & \mathbf{q}_\mathbf{\chi} \\
\mathbf{q}^T_\mathbf{\chi} & q_{0,\mathbf{\chi}}
\end{bmatrix}
where :math:`\mathbf{q}_\mathbf{\chi}` is a six-element vector and
:math:`q_{0,\mathbf{\chi}}` is a scalar. Substituting into our squared error
function gives
.. math::
\epsilon_\mathbf{\chi} =
\mathbf{a}^T \mathbf{Q}_\mathbf{\chi} \mathbf{a} +
2 \mathbf{a}^T \mathbf{q}_\mathbf{\chi} + q_{0,\mathbf{\chi}}.
To minimize, we differentiate and set to zero. Hence,
.. math::
\nabla_\mathbf{a} \epsilon_\mathbf{\chi} =
2 \mathbf{Q}_\mathbf{\chi} \mathbf{a} + 2 \mathbf{q}_\mathbf{\chi} = 0
and so the local affine parameter vector satisfies
.. math::
\mathbf{Q}_\mathbf{\chi} \mathbf{a}_\mathbf{\chi} = - \mathbf{q}_\mathbf{\chi}.
In our implementation, we avoid calculating the inverse of
:math:`\mathbf{Q}_\mathbf{\chi}` directly and solve this equation by
eigenvector decomposition.
Iteration
'''''''''
There are three stres in the full registration algorithm: transform the images
to the DTCWT domain, perform motion estimation and register the source image.
We do this via an iterative process where coarse-scale estimates of
:math:`\mathbf{a}_\mathbf{\chi}` are estimated from coarse-scale levels of the
transform and progressively refined with finer-scale levels.
The following flow diagram, taken from the paper, illustrates the algorithm.
.. image:: registration-flow.png
:class: align-center
The pair of images to be registered are first transformed by the DTCWT and
levels to be used for motion estimation are selected. The subband coefficients
of the source image are shifted according to the current motion field estimate.
These shifted coefficients together with those of the reference image are then
used to generate motion constraints. From these the
:math:`\mathbf{\tilde{Q}}_\mathbf{\chi}` matrices are calculated and the local
affine distortion parameters updated. After a few iterations, the distortion
parameters are used to warp the source image directly.
Using the implementation
------------------------
The implementation of the image registration algorithm is accessed via the
:py:mod:`dtcwt.registration` module's functions. The two functions of most
interest at :py:func:`dtcwt.registration.estimatereg` and
:py:func:`dtcwt.registration.warp`. The former will estimate
:math:`\mathbf{a}_\mathbf{\chi}` for each 8x8 block in the image and
:py:func:`dtcwt.registration.warp` will take these affine parameter vectors and
warp an image with them.
As an example, we will register two frames from a video of road traffic.
Firstly, as boilerplate, import plotting command from pylab and also the
:py:mod:`datasets` module which is part of the test suite for :py:mod:`dtcwt`.
.. code::
from pylab import *
import datasets
If we show one image in the red channel and one in the green, we can see where
the images are incorrectly registered by looking for red or green fringes:
.. code::
ref, src = datasets.regframes('traffic')
figure()
imshow(np.dstack((ref, src, np.zeros_like(ref))))
title('Registration input images')
.. plot::
from pylab import *
import datasets
ref, src = datasets.regframes('traffic')
figure()
imshow(np.dstack((ref, src, np.zeros_like(ref))))
title('Registration input images')
To register the images we first take the DTCWT:
.. code::
import dtcwt
transform = dtcwt.Transform2d()
ref_t = transform.forward(ref, nlevels=6)
src_t = transform.forward(src, nlevels=6)
Registration is now performed via the :py:func:`dtcwt.registration.estimatereg`
function. Once the registration is estimated, we can warp the source image to
the reference using the :py:func:`dtcwt.registration.warp` function.
.. code::
import dtcwt.registration as registration
reg = registration.estimatereg(src_t, ref_t)
warped_src = registration.warp(src, reg, method='bilinear')
Plotting the warped and reference image in the green and red channels again
shows a marked reduction in colour fringes.
.. code::
figure()
imshow(np.dstack((ref, warped_src, np.zeros_like(ref))))
title('Source image warped to reference')
.. plot::
from pylab import *
import datasets
ref, src = datasets.regframes('traffic')
import dtcwt
transform = dtcwt.Transform2d()
ref_t = transform.forward(ref, nlevels=6)
src_t = transform.forward(src, nlevels=6)
import dtcwt.registration as registration
reg = registration.estimatereg(src_t, ref_t)
warped_src = registration.warp(src, reg, method='bilinear')
figure()
imshow(np.dstack((ref, warped_src, np.zeros_like(ref))))
title('Source image warped to reference')
The velocity field, in units of image width/height, can be calculated by the
:py:func:`dtcwt.registration.velocityfield` function. We need to scale the
result by the image width and height to get a velocity field in pixels.
.. code::
vxs, vys = registration.velocityfield(reg, ref.shape[:2], method='bilinear')
vxs = vxs * ref.shape[1]
vys = vys * ref.shape[0]
We can plot the result as a quiver map overlaid on the reference image:
.. code::
figure()
X, Y = np.meshgrid(np.arange(ref.shape[1]), np.arange(ref.shape[0]))
imshow(ref, cmap=cm.gray, clim=(0,1))
step = 8
quiver(X[::step,::step], Y[::step,::step],
vxs[::step,::step], vys[::step,::step],
color='g', angles='xy', scale_units='xy', scale=0.25)
title('Estimated velocity field (x4 scale)')
.. plot::
from pylab import *
import datasets
ref, src = datasets.regframes('traffic')
import dtcwt
transform = dtcwt.Transform2d()
ref_t = transform.forward(ref, nlevels=6)
src_t = transform.forward(src, nlevels=6)
import dtcwt.registration as registration
reg = registration.estimatereg(src_t, ref_t)
warped_src = registration.warp(src, reg, method='bilinear')
vxs, vys = registration.velocityfield(reg, ref.shape[:2], method='bilinear')
vxs = vxs * ref.shape[1]
vys = vys * ref.shape[0]
figure()
X, Y = np.meshgrid(np.arange(ref.shape[1]), np.arange(ref.shape[0]))
imshow(ref, cmap=cm.gray, clim=(0,1))
step = 8
quiver(X[::step,::step], Y[::step,::step],
vxs[::step,::step], vys[::step,::step],
color='g', angles='xy', scale_units='xy', scale=0.25)
title('Estimated velocity field (x4 scale)')
We can also plot the magnitude of the velocity field which clearly shows the moving cars:
.. code::
figure()
imshow(np.abs(vxs + 1j*vys), cmap=cm.hot)
title('Velocity field magnitude')
.. plot::
from pylab import *
import datasets
ref, src = datasets.regframes('traffic')
import dtcwt
transform = dtcwt.Transform2d()
ref_t = transform.forward(ref, nlevels=6)
src_t = transform.forward(src, nlevels=6)
import dtcwt.registration as registration
reg = registration.estimatereg(src_t, ref_t)
warped_src = registration.warp(src, reg, method='bilinear')
vxs, vys = registration.velocityfield(reg, ref.shape[:2], method='bilinear')
vxs = vxs * ref.shape[1]
vys = vys * ref.shape[0]
figure()
imshow(np.abs(vxs + 1j*vys), cmap=cm.hot)
title('Velocity field magnitude')
|