def __init__(self,params):
self.optional_params = None
self.frame_id_to_param_no = {}
correction_vectors.__init__(self)
# XXX Set in mark0.correction_vectors.read_data()
#self.nominal_tile_centers(params.effective_tile_boundaries)
self.params = params
self.read_data(params)
# for eventual write-out, deep copy the input:
self.OUTPUT = copy.deepcopy(self.FRAMES)
if params.max_frames==None:
FR_LIMIT = len(self.FRAMES["frame_id"]) # don't adjust for degrees of freedom
self.n_refined_frames = FR_LIMIT
else:
self.n_refined_frames = params.max_frames
# XXX CHECK THIS BLOCK MORE CAREFULLY!
mark5_iteration.__init__(self)
self.tile_translations=self.register(
"tile_trans",ndata=len(self.tiles) // 4,kdim=2,data=[0.]*(len(self.tiles) // 2)) # x & y displacements for each of 64 tiles
self.tile_rotations=self.register("tile_rot",ndata=len(self.tiles) // 4,data=[0.]*(len(self.tiles) // 4))
self.frame_translations=self.register(
"frame_trans",ndata=self.n_refined_frames,kdim=2,data=[0.]*(2*self.n_refined_frames))
self.frame_distances=self.register("frame_distance",
ndata=self.n_refined_frames,data=[0.]*self.n_refined_frames)
self.frame_rotz=self.register("frame_rotz",
ndata=self.n_refined_frames,data=[0.]*self.n_refined_frames)
self.frame_roty=self.register_local("frame_roty",
ndata=self.n_refined_frames,data=[0.]*self.n_refined_frames)
self.frame_rotx=self.register_local("frame_rotx",
ndata=self.n_refined_frames,data=[0.]*self.n_refined_frames)
self.mean_energy_factor=self.register_local("mean_energy_factor",
ndata=self.n_refined_frames,data=[1.]*self.n_refined_frames)
self.bandpass_logfac=self.register_local("bandpass_logfac",
ndata=self.n_refined_frames,data=[0.]*self.n_refined_frames)
self.mosaicity_factor=self.register_local("mosaicity_factor",
ndata=self.n_refined_frames,data=[1.]*self.n_refined_frames)
self.g_factor=self.register_local("g_factor",
ndata=self.n_refined_frames,kdim=6,data=[1.]*6*self.n_refined_frames)
self.vector_data = vector_collection(self.frame_id, self.HKL)
self.jacobian_frame_roty = self.vector_data.register(tag="frame_roty")
self.jacobian_frame_rotx = self.vector_data.register(tag="frame_rotx")
"""0. Read in only 500 frames, refine only 20
1. Define the new parameter here.
2. Define its new behavior in parameter_based_function()
3. set use_curvatures=False
4. implement refinement with finite differences:
include the array name in setting compute_finite_difference_gradients_if_requested()
fix the requirement for "zip"
verify fd_gradients go to zero upon convergence
verify parameter vector has reasonable values
5. implement analytic gradients, list out comparison columns
6. document the gradients in a tex file
7. implement curvatures & flag them in here
"""
self.x = self.as_x_array()
def __init__(self,params):
correction_vectors.__init__(self)
self.read_data(params)
self.x = flex.double([0.]*128) # x & y displacements for each of 64 tiles
lbfgs_with_curvatures_mix_in.__init__(self,
min_iterations=0,
max_iterations=1000,
use_curvatures=True)
def __init__(self,params):
self.bandpass_models = {}
correction_vectors.__init__(self)
#self.nominal_tile_centers(params.effective_tile_boundaries)
self.read_data(params)
self.params = params
self.x = flex.double([0.]*(len(self.tiles) // 2)+[0.]*(len(self.tiles) // 4)) # x & y displacements for each of 64 tiles
lbfgs_with_curvatures_mix_in.__init__(self,
min_iterations=0,
max_iterations=1000,
use_curvatures=True)
def __init__(self, params):
self.bandpass_models = {}
correction_vectors.__init__(self)
#self.nominal_tile_centers(params.effective_tile_boundaries)
self.read_data(params)
self.params = params
self.x = flex.double(
[0.] * (len(self.tiles) // 2) + [0.] *
(len(self.tiles) // 4)) # x & y displacements for each of 64 tiles
lbfgs_with_curvatures_mix_in.__init__(self,
min_iterations=0,
max_iterations=1000,
use_curvatures=True)
def __init__(self, params):
correction_vectors.__init__(self)
self.read_data(params)
self.x = flex.double([0.0] * 128) # x & y displacements for each of 64 tiles
lbfgs_with_curvatures_mix_in.__init__(self, min_iterations=0, max_iterations=1000, use_curvatures=True)
