def determine_slice_flip(morphology: Morphology, soma_marker: Dict,
slice_image_flip: bool):
"""
Determines whether the tilt correction should be positive or negative
Parameters
----------
morphology: Morphology object
soma_marker: soma marker dictionary from reconstruction marker file
slice_image_flip: indicates whether the image was flipped relative
to the slice (e.g the z axis of the image is opposite
to the z axis in the slice)
Returns
-------
flip_toggle -1 or 1 to be multiplied against tilt correction
"""
flip_toggle = 1
morph_soma = morphology.get_soma()
if (soma_marker['z'] - morph_soma['z']) > 0:
flip_toggle = -1
if flip_toggle == 1 and not slice_image_flip:
flip_toggle *= -1
return flip_toggle
def calculate_transform(
gradient_field: xr.DataArray,
morph: Morphology,
node: Optional[List[float]] = None,
):
theta = get_upright_angle(gradient_field, node)
transform = np.eye(4)
transform[0:3, 0:3] = aff.rotation_from_angle(theta)
soma = morph.get_soma()
cos_theta = np.cos(theta)
sin_theta = np.sin(theta)
transform[0:3, 3] = np.asarray([
-soma["x"] * cos_theta + soma["y"] * sin_theta + soma["x"],
-soma["x"] * sin_theta - soma["y"] * cos_theta + soma["y"], 0
])
output = {
'upright_transform': aff.AffineTransform(transform),
'upright_angle': theta
}
return output
def estimate_scale_correction(morphology: Morphology,
soma_depth: float,
soma_marker_z: float,
cut_thickness: Optional[float] = 350):
"""
Estimate a scale factor to correct the reconstructed morphology
for slice shrinkage
Prior to reconstruction, the slice shrinks due to evaporation.
This is most notable in the z axis, which is the slice thickness.
To correct for shrinkage we compare soma depth within the slice
obtained soon after cutting the slice to the fixed_soma_depth obtained
during the reconstruction. Then the scale correction is estimated as:
scale = soma_depth / fixed_soma_depth.
This is sensible as long as the z span of the corrected reconstruction
is contained within the slice thickness. Thus we also estimate
the maximum scale correction as:
scale_max = cut_thickness / z_span,
and take the smaller of scale and scale_max
Parameters
----------
morphology: Morphology object
soma_depth: recorded depth of the soma when it was sliced
soma_marker_z: soma marker z value from revised marker file
(z is on the slice surface for the marker file)
cut_thickness: thickness of the cut slice
Returns
-------
scale factor correction
"""
soma_morph_z = morphology.get_soma()['z']
fixed_depth = np.abs(soma_morph_z - soma_marker_z)
scale = soma_depth / fixed_depth
node_z = [node['z'] for node in morphology.nodes()]
z_range = np.max(node_z) - np.min(node_z)
scale_max = cut_thickness / z_range
if scale > scale_max:
scale = scale_max
warnings.warn(f"Shrinkage scale correction factor: {scale} "
f"exceeded the max allowed value: {scale_max}. "
f"Will correct for shrinkage using the maximum value."
)
return scale