xfel.metrology package

Subpackages

Submodules

xfel.metrology.flatfile module

For Mikhail:

Quad 3, pair 0 should have S2 20907 (not 20904).

Quad 3, pair 4 should have L2 43477 (not 43476), but that may be rounding error.

Quad 3, pair 0 has L2 43857 which is 300 um longer than others

XXX Really need to be able to visualise this in 3D!

Other open issues:

Possible to participate in next optical measurement?

Is the center of the rectangle the center of the pixel arrays?

class xfel.metrology.flatfile.optimise_rectangle(vertices, weights, c, u, v, l)

Bases: object

Misnomer, optimises everything.

compute_functional_and_gradients()

Compute sum of squared residual, and derivatives of theta, slow, and fast. XXX THIS IS ALL DIFFERENT FROM MY PEN-AND-PAPER WORK

class xfel.metrology.flatfile.optimise_rectangle_2(vertices, weights, c, u, v, l)

Bases: object

Misnomer, optimises everything.

compute_functional_and_gradients()

Compute sum of squared residual, and derivatives of theta, slow, and fast. XXX THIS IS ALL DIFFERENT FROM MY PEN-AND-PAPER WORK

class xfel.metrology.flatfile.optimise_rectangle_3(vertices, weights, u, v, side_long, side_short)

Bases: object

compute_functional_and_gradients()
while True:

t = self.x[0]**2 + self.x[1]**2 + self.x[2]**2 + self.x[3]**2

# print “Got weights”, self.x[0]**2 / t, self.x[1]**2 / t, self.x[2]**2 / t, self.x[3]**2 / t

for i in range(4):

w = self.x[i]**2 / t

ok = True self.x[i] = math.sqrt(w) if w > 0.35:

self.x[i] = 0.3 / w * math.sqrt(w) ok = False

if ok:

break

xfel.metrology.flatfile.parse_metrology(path, detector='CxiDs1', plot=True, do_diffs=True, old_style_diff_path=None)

Measurement file has all units in micrometers. The coordinate system is right-handed XXX verify this. The origin is at the lower, left corner of sensor 1. XXX Are quadrants still 0, 1, 2, 3 in counter-clockwise order beginning at top left corner?

xfel.metrology.mark0 module

Main idea: having already done

  1. indexing & integration –> allresults

  2. metrology assessment –> mysql store tag_spotfinder

  3. cxi.merge –> mysql store tag_frame

…now do a detailed metrology refinement to simultaneously optimize metrology and crystal orientation.

xfel.metrology.mark0.consistency_controls(DATA, params, annotate=False)
class xfel.metrology.mark0.correction_vectors

Bases: correction_vector_store

DETECTOR_NORMAL = (0.0, 0.0, -1.0)
INCIDENT_BEAM = (0.0, 0.0, -1.0)
delrsq_functional(calcx, calcy)
get_frames_from_mysql(params)
get_obs_from_mysql(params)
print_table()
read_data(params)
static standalone_check(self, setting_id, entry, d, cutoff)
tile_weight(idx)
xfel.metrology.mark0.get_phil(args)
xfel.metrology.mark0.run(args)

xfel.metrology.mark1 module

class xfel.metrology.mark1.fit_translation(params)

Bases: correction_vectors, lbfgs_with_curvatures_mix_in

compute_functional_and_gradients()
curvatures()
post_min_recalc()
print_table()
xfel.metrology.mark1.run(args)

xfel.metrology.mark10 module

class xfel.metrology.mark10.fit_translation4(params)

Bases: mark5_iteration, fit_translation2

compute_finite_difference_gradients_if_requested()
compute_functional_and_gradients()
detector_origin_analysis()
jacobian_frame_rotx

  1. Read in only 500 frames, refine only 20

  2. Define the new parameter here.

  3. Define its new behavior in parameter_based_function()

  4. set use_curvatures=False

  5. 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

  6. implement analytic gradients, list out comparison columns

  7. document the gradients in a tex file

  8. implement curvatures & flag them in here

parameter_based_model(params)
parameter_based_model_one_frame_detail(frame_id, iframe, all_model)
print_table()
print_table_2()
static print_unit_translations(data, params, optional)
radial_transverse_analysis()
run_cycle_a()
run_cycle_b(iteration)
same_sensor_table(verbose=True)

xfel.metrology.mark3 module

class xfel.metrology.mark3.fit_translation2(params)

Bases: fit_translation

compute_functional_and_gradients()
curvatures()
nominal_tile_centers(corners)
parameter_based_model(params)
post_min_recalc()
print_table()
same_sensor_table(verbose=True)
xfel.metrology.mark3.run(args)

xfel.metrology.quadrant module

class xfel.metrology.quadrant.one_panel(image, panel, i_quad, quad, plot=False, multi_angle=True, plot_range=None, show=True)

Bases: object

CC(beam_center, rotmat=None)
class xfel.metrology.quadrant.one_sensor(image, sensor, manager)

Bases: object

CC(beam_center)

Module contents