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Code formatting

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This commit is contained in:
Joel Collins 2020-04-28 13:42:26 +01:00
parent 9ff24e8e37
commit 1a6088a816
1 changed files with 31 additions and 22 deletions
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21
openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_2d.py
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@ -14,6 +14,7 @@ from camera_stage_tracker import Tracker, move_until_motion_detected
from functools import partial from functools import partial
def backlash_corrected_move(get_position, move, backlash_amount, pos): def backlash_corrected_move(get_position, move, backlash_amount, pos):
"""Make two moves, arriving at `pos` from a consistent direction""" """Make two moves, arriving at `pos` from a consistent direction"""
displacement = pos - get_position() displacement = pos - get_position()
@ -22,10 +23,12 @@ def backlash_corrected_move(get_position, move, backlash_amount, pos):
move(pos - backlash_vector) move(pos - backlash_vector)
move(pos) move(pos)
def bake_backlash_corrected_move(get_position, move, backlash_amount): def bake_backlash_corrected_move(get_position, move, backlash_amount):
"""Return a function that performs backlash-corrected moves""" """Return a function that performs backlash-corrected moves"""
return partial(backlash_corrected_move, get_position, move, backlash_amount) return partial(backlash_corrected_move, get_position, move, backlash_amount)
def calibrate_xy_grid(tracker, move, step=100, n_steps=4, backlash_compensation=0): def calibrate_xy_grid(tracker, move, step=100, n_steps=4, backlash_compensation=0):
"""Make a series of moves in X and Y to determine the XY components of the pixel-to-sample matrix. """Make a series of moves in X and Y to determine the XY components of the pixel-to-sample matrix.
@ -63,19 +66,25 @@ def calibrate_xy_grid(tracker, move, step = 100, n_steps=4, backlash_compensatio
image_positions -= np.mean(image_positions, axis=0) image_positions -= np.mean(image_positions, axis=0)
# image_positions *= -1 # To get the matrix right, we want the position of each # image_positions *= -1 # To get the matrix right, we want the position of each
# image relative to the template, rather than the other way around # image relative to the template, rather than the other way around
A, res, rank, s = np.linalg.lstsq(image_positions, stage_positions) # we solve pixel_shifts*A = location_shifts A, res, rank, s = np.linalg.lstsq(
image_positions, stage_positions
) # we solve pixel_shifts*A = location_shifts
transformed_image_positions = np.dot(image_positions, A) transformed_image_positions = np.dot(image_positions, A)
residuals = transformed_image_positions - stage_positions residuals = transformed_image_positions - stage_positions
fractional_error = norm(residuals) / stage_positions.shape[0] step fractional_error = norm(residuals) / stage_positions.shape[0]
print(f"Ratio of residuals to displacement is {fractional_error})") print(f"Ratio of residuals to displacement is {fractional_error})")
if fractional_error > 0.05: # Check it was a reasonably good fit if fractional_error > 0.05: # Check it was a reasonably good fit
print("Warning: the error fitting measured displacements was %.1f%%" % (fractional_error*100)) print(
print(f"Calibrated the pixel-location matrix.\nResiduals were {fractional_error*100:.1f}% of the shift.") "Warning: the error fitting measured displacements was %.1f%%"
% (fractional_error * 100)
)
print(
f"Calibrated the pixel-location matrix.\nResiduals were {fractional_error*100:.1f}% of the shift."
)
return { return {
"image_to_stage_displacement": A, "image_to_stage_displacement": A,
"moves": (stage_positions, image_positions), "moves": (stage_positions, image_positions),
"fractional_error": fractional_error "fractional_error": fractional_error,
} }