def __init__(self, output_dir, config_name, letter_match=None):
self.num_points = None
self.domain_max = None
self.dx = None
self.verbose_file_output = False
self.output_dir = output_dir
self.spline_interp = False
# used only for letter examples
self.letter_match = letter_match
smoothImageConfig.configure(self, config_name)
self.rg = regularGrid.RegularGrid(self.dim, self.num_points, \
self.domain_max, self.dx, "meta")
self.times = numpy.linspace(self.time_min, self.time_max, \
self.num_times)
self.dt = (self.time_max - self.time_min) / (self.num_times - 1)
self.optimize_iteration = 0
self.g_eps = 1.
logging.info("sigma: %f" % self.sigma)
logging.info("sfactor: %f" % self.sfactor)
logging.info("num_points: %s" % str(self.rg.num_points))
logging.info("domain_max: %s" % str(self.rg.domain_max))
logging.info("dx: %s" % str(self.rg.dx))
logging.info("dt: %f" % self.dt)
rg = self.rg
self.x0 = self.rg.nodes.copy()
self.xt = numpy.zeros((rg.num_nodes, 3, self.num_times))
self.v = numpy.zeros((rg.num_nodes, 3, self.num_times))
self.m = numpy.zeros((rg.num_nodes, self.num_times))
self.z = numpy.zeros((rg.num_nodes, 3, self.num_times))
self.J = numpy.ones((rg.num_nodes, self.num_times))
self.id_x = self.rg.nodes[:,0].copy()
self.id_y = self.rg.nodes[:,1].copy()
self.m = numpy.zeros((rg.num_nodes, self.num_times))
self.alpha = numpy.zeros(rg.num_nodes)
self.alpha_state = numpy.zeros_like(self.alpha)
rg.create_vtk_sg()
rg.add_vtk_point_data(self.template_in, "template_in")
rg.add_vtk_point_data(self.target_in, "target_in")
rg.vtk_write(0, "images", output_dir=self.output_dir)
if self.spline_interp:
si = SplineInterp(rg, self.KH, self.template_in)
self.dual_template = si.minimize()
si = SplineInterp(rg, self.KH, self.target_in)
self.dual_target = si.minimize()
else:
self.dual_template = self.template_in.copy()
self.dual_target = self.target_in.copy()
(templ, dtempl) = kernelMatrix_fort.applyk_and_diff( \
rg.nodes, rg.nodes, self.dual_template,
self.khs, self.kho, self.rg.num_nodes)
self.target = kernelMatrix_fort.applyk( \
rg.nodes, rg.nodes, self.dual_target,
self.khs, self.kho, self.rg.num_nodes)
self.template = templ
self.D_template = dtempl
if True:
temp = numpy.zeros(rg.num_nodes)
temp[50] = 1.
kvt = kernelMatrix_fort.applyk( \
rg.nodes, rg.nodes, temp,
self.kvs, self.kvo, self.rg.num_nodes)
kht = kernelMatrix_fort.applyk( \
rg.nodes, rg.nodes, temp,
self.khs, self.kho, self.rg.num_nodes)
rg.create_vtk_sg()
rg.add_vtk_point_data(self.template, "template")
rg.add_vtk_point_data(self.D_template, "D_template")
rg.add_vtk_point_data(self.target, "target")
rg.add_vtk_point_data(kvt, "kvt")
rg.add_vtk_point_data(kht, "kht")
rg.vtk_write(0, "initial_data", output_dir=self.output_dir)
tmpMax = numpy.max(numpy.abs(self.template))
tarMax = numpy.max(numpy.abs(self.target))
self.template /= tmpMax
self.dual_template /= tmpMax
self.target /= tarMax
self.dual_target /= tarMax
def __init__(self, output_dir, config_name, letter_match=None):
self.num_points = None
self.domain_max = None
self.dx = None
self.verbose_file_output = False
self.output_dir = output_dir
self.spline_interp = False
self.noJ = True
self.unconstrained = False
# used only for letter examples
self.letter_match = letter_match
smoothImageConfig.configure(self, config_name)
self.rg = regularGrid.RegularGrid(self.dim, self.num_points, \
self.domain_max, self.dx, "meta")
self.times = numpy.linspace(self.time_min, self.time_max, \
self.num_times)
self.dt = (self.time_max - self.time_min) / (self.num_times - 1)
self.optimize_iteration = 0
self.g_eps = 1.
self.khSmooth =0.2*numpy.asarray(self.rg.dx).max() # self.khs/2
logging.info("sigma: %f" % self.sigma)
logging.info("sfactor: %f" % self.sfactor)
logging.info("num_points: %s" % str(self.rg.num_points))
logging.info("domain_max: %s" % str(self.rg.domain_max))
logging.info("dx: %s" % str(self.rg.dx))
logging.info("dt: %f" % self.dt)
logging.info('khSmooth: %f'% self.khSmooth)
rg = self.rg
self.x0 = self.rg.nodes.copy()
self.xt = numpy.zeros((rg.num_nodes, 3, self.num_times))
self.v = numpy.zeros((rg.num_nodes, 3, self.num_times))
self.m = numpy.zeros((rg.num_nodes, self.num_times))
self.z = numpy.zeros((rg.num_nodes, 3, self.num_times))
self.id_x = self.rg.nodes[:,0].copy()
self.id_y = self.rg.nodes[:,1].copy()
self.m = numpy.zeros((rg.num_nodes, self.num_times))
self.alpha = numpy.zeros(rg.num_nodes)
self.alpha_state = numpy.zeros_like(self.alpha)
if self.unconstrained:
self.noJ = True
self.z0 = numpy.zeros((rg.num_nodes, 3))
self.z0weight = 100*numpy.ones((rg.num_nodes,1))
self.z0_state = numpy.zeros((rg.num_nodes, 3))
if not self.noJ:
self.J = numpy.ones((rg.num_nodes, self.num_times))
rg.create_vtk_sg()
rg.add_vtk_point_data(self.template_in, "template_in")
rg.add_vtk_point_data(self.target_in, "target_in")
rg.vtk_write(0, "images", output_dir=self.output_dir)
if self.spline_interp:
trg = kernelMatrix_fort.applyk( \
rg.nodes, rg.nodes, self.target_in,
self.khs/4, self.kho, self.rg.num_nodes)
tpl = kernelMatrix_fort.applyk( \
rg.nodes, rg.nodes, self.template_in,
self.khs/4, self.kho, self.rg.num_nodes)
self.khSmooth = self.khs
logging.info('RKHS Projection Template')
si = SplineInterp(rg, self.khs, self.kho, tpl,True)
self.dual_template = si.minimize()
logging.info('RKHS Projection Target')
si = SplineInterp(rg, self.khs, self.kho, trg)
self.dual_target = si.minimize()
else:
self.dual_template = self.template_in.copy()
self.dual_target = self.target_in.copy()
(templ, dtempl) = kernelMatrix_fort.applyk_and_diff( \
rg.nodes, rg.nodes, self.dual_template,
self.khSmooth, self.kho, self.rg.num_nodes)
self.target = kernelMatrix_fort.applyk( \
rg.nodes, rg.nodes, self.dual_target,
self.khSmooth, self.kho, self.rg.num_nodes)
self.template = templ
self.D_template = dtempl
if True:
temp = numpy.zeros(rg.num_nodes)
temp[rg.num_nodes/2 + rg.num_points[1]/2] = 1.
kvt = kernelMatrix_fort.applyk( \
rg.nodes, rg.nodes, temp,
self.kvs, self.kvo, self.rg.num_nodes)
kht = kernelMatrix_fort.applyk( \
rg.nodes, rg.nodes, temp,
self.khs, self.kho, self.rg.num_nodes)
rg.create_vtk_sg()
rg.add_vtk_point_data(self.template, "template")
rg.add_vtk_point_data(self.D_template, "D_template")
rg.add_vtk_point_data(self.target, "target")
rg.add_vtk_point_data(kvt, "kvt")
rg.add_vtk_point_data(kht, "kht")
rg.vtk_write(0, "initial_data", output_dir=self.output_dir)
tmpMax = numpy.max(numpy.abs(self.template))
tarMax = numpy.max(numpy.abs(self.target))
self.D_template /= tmpMax
self.template /= tmpMax
self.dual_template /= tmpMax
self.target /= tarMax
self.dual_target /= tarMax
self.z0weight[:] = numpy.sqrt(1e-6 + (self.D_template**2).sum(axis=1)[..., numpy.newaxis])
