cylindra.components
CylSpline
Bases: Spline
A spline object with cylindrical structure.
Source code in cylindra/components/spline/_cyl_spline.py
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|
orientation: Ori
property
writable
Orientation of the spline.
radius: nm | None
property
writable
Average radius of the cylinder.
clip(start, stop)
Clip spline and generate a new one.
This method does not convert spline bases. _lims
is updated instead.
For instance, if you want to clip spline at 20% to 80% position, call
spl.clip(0.2, 0.8)
. If stop < start
, the orientation of spline
will be inverted, thus the orientation
attribute will also be inverted.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
start |
float
|
New starting position. |
required |
stop |
float
|
New stopping position. |
required |
Returns:
Type | Description |
---|---|
CylSpline
|
Clipped spline. |
Source code in cylindra/components/spline/_cyl_spline.py
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cylinder_model(offsets=(0.0, 0.0), **kwargs)
Return the cylinder model of the spline.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
offsets |
tuple of float
|
Offset of the model. See :meth: |
(0.0, 0.0)
|
Returns:
Type | Description |
---|---|
CylinderModel
|
The cylinder model. |
Source code in cylindra/components/spline/_cyl_spline.py
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cylinder_params(**kwargs)
Get the cylinder parameters of the spline.
Source code in cylindra/components/spline/_cyl_spline.py
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invert()
Invert the direction of spline. Also invert orientation if exists.
Returns:
Type | Description |
---|---|
CylSpline
|
Inverted object |
Source code in cylindra/components/spline/_cyl_spline.py
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nrise(**kwargs)
Raw start number (minus for microtubule)
Source code in cylindra/components/spline/_cyl_spline.py
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radius_range(rc=None)
Return the range of the radius used for the cylindric coordinate.
Source code in cylindra/components/spline/_cyl_spline.py
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restore()
Restore the original, not-clipped spline.
Returns:
Type | Description |
---|---|
Spline
|
Copy of the original spline. |
Source code in cylindra/components/spline/_cyl_spline.py
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update_glob_by_cylinder_params(cparams)
Update the global properties using a CylinderParameters object.
Source code in cylindra/components/spline/_cyl_spline.py
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update_props(*, npf=None, start=None, orientation=None)
Update the npf or orientation parameters in place.
Source code in cylindra/components/spline/_cyl_spline.py
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Spline
Bases: BaseComponent
3D spline curve model with coordinate system.
Anchor points can be set via anchor
property. A spline object is semi-immutable.
Different spline curves are always of different objects, but the anchors and
properties can be dynamically changed.
References
- Scipy document https://docs.scipy.org/doc/scipy/reference/generated/scipy.interpolate.splprep.html
Source code in cylindra/components/spline/_spline_base.py
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anchors: NDArray[np.float32]
deletable
property
writable
Local anchors along spline.
coeff: list[np.ndarray]
property
Spline coefficient.
config: SplineConfig
property
Return the spline configuration
extrapolate: ExtrapolationMode
property
Extrapolation mode of the spline.
has_anchors: bool
property
True if there are any anchors.
knots: np.ndarray
property
Spline knots.
lims: tuple[float, float]
property
Return spline limit positions.
order: int
property
Spline order.
params: np.ndarray
property
Spline parameters.
props: SplineProps
property
Return the spline properties
__repr__()
Use start/end points to describe a spline.
Source code in cylindra/components/spline/_spline_base.py
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anchors_to_molecules(positions=None, rotation=None)
Convert coordinates of anchors to Molecules
instance.
Coordinates of anchors must be in range from 0 to 1. The y-direction of
Molecules
always points at the direction of spline and the z- direction always
in the plane orthogonal to YX-plane.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
positions |
iterable of float
|
Positions. Between 0 and 1. If not given, anchors are used instead. |
None
|
Returns:
Type | Description |
---|---|
Molecules
|
Molecules object of points. |
Source code in cylindra/components/spline/_spline_base.py
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cartesian(shape, s_range=(0, 1), scale=1.0)
Generate a Cartesian coordinate system along spline that can be used for
ndi.map_coordinate
. Note that this coordinate system is distorted, thus
does not reflect real geometry (such as distance and derivatives).
Parameters:
Name | Type | Description | Default |
---|---|---|---|
shape |
(float, float)
|
The ZX-shape of output coordinate system. Center of the array will be spline curve itself after coodinate transformation. |
required |
s_range |
tuple[float, float]
|
Range of spline. Spline coordinate system will be built between
|
(0, 1)
|
scale |
nm
|
Scale of coordinates, i.e. spacing of the grid. |
1.0
|
Returns:
Type | Description |
---|---|
ndarray
|
(V, S, H, D) shape. Each cooresponds to vertical, longitudinal, horizontal and dimensional axis. |
Source code in cylindra/components/spline/_spline_base.py
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cartesian_to_world(coords, nknots=512)
Inverse Cartesian coordinate mapping, (z', y', x') to world coordinate.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
coords |
ndarray
|
Spline Cartesian coordinates. All the coordinates must be in nm unit. |
required |
Returns:
Type | Description |
---|---|
ndarray
|
World coordinates. |
Source code in cylindra/components/spline/_spline_base.py
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clip(start, stop)
Clip spline and generate a new one.
This method does not convert spline bases. _lims
is updated instead.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
start |
float
|
New starting position. |
required |
stop |
float
|
New stopping position. |
required |
Returns:
Type | Description |
---|---|
Spline
|
Clipped spline. |
Source code in cylindra/components/spline/_spline_base.py
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close_to(other)
True if two objects draws the same curve.
Source code in cylindra/components/spline/_spline_base.py
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copy(copy_props=True, copy_config=True)
Copy Spline object.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
copy_props |
bool
|
Also copy local/global properties if true. |
True
|
Returns:
Type | Description |
---|---|
Spline
|
Copied object. |
Source code in cylindra/components/spline/_spline_base.py
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curvature(positions=None)
Calculate curvature of spline curve.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
positions |
sequence of float
|
Positions. Between 0 and 1. If not given, anchors are used instead. |
None
|
Returns:
Type | Description |
---|---|
ndarray
|
Array of curvature. |
References
- https://en.wikipedia.org/wiki/Curvature#Space_curves
Source code in cylindra/components/spline/_spline_base.py
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curvature_radii(positions=None)
Inverse of curvature.
Source code in cylindra/components/spline/_spline_base.py
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cylindrical(r_range, s_range=(0, 1), scale=1.0)
Generate a cylindrical coordinate system along spline that can be used for
ndi.map_coordinate
. Note that this coordinate system is distorted, thus
does not reflect real geometry (such as distance and derivatives).
Parameters:
Name | Type | Description | Default |
---|---|---|---|
r_range |
(nm, nm)
|
Range of radius in nm. r=0 will be spline curve itself after coodinate transformation. |
required |
s_range |
tuple[float, float]
|
Range of spline. Spline coordinate system will be built between
|
(0, 1)
|
scale |
nm
|
Scale of coordinates, i.e. spacing of the grid. |
1.0
|
Returns:
Type | Description |
---|---|
ndarray
|
(V, S, H, D) shape. Each cooresponds to radius, longitudinal, angle and dimensional axis. |
Source code in cylindra/components/spline/_spline_base.py
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cylindrical_to_molecules(coords)
Convert coordinates of points near the spline to Molecules
instance.
Coordinates of points must be those in spline cylindrical coordinate system.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
coords |
(N, 3) array
|
Spline cylindrical coordinates of points. |
required |
Returns:
Type | Description |
---|---|
Molecules
|
Molecules object of points. |
Source code in cylindra/components/spline/_spline_base.py
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cylindrical_to_world(coords)
Inverse cylindrical coordinate mapping, (r, y, angle) to world coordinate.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
coords |
ndarray
|
Cylindrical coordinates. "r" and "y" must be in scale of "nm", while angle must be in radian. |
required |
Returns:
Type | Description |
---|---|
ndarray
|
World coordinates. |
Source code in cylindra/components/spline/_spline_base.py
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distances(positions=None, nknots=512)
Get the distances from u=0.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
positions |
sequence of float
|
Positions. Between 0 and 1. If not given, anchors are used instead. |
None
|
Returns:
Type | Description |
---|---|
ndarray
|
Distances for each |
Source code in cylindra/components/spline/_spline_base.py
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fit(coords, *, err_max=1.0)
Fit spline model to coordinates.
This method uses scipy.interpolate.splprep
to fit given coordinates to a
spline.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
coords |
ndarray
|
Coordinates. Must be (N, 3). |
required |
err_max |
float
|
Error allowed for fitting. Several upper limit of residual values will be used and the fit that results in error lower than this value and minimize the maximum curvature will be chosen. |
1.0
|
Returns:
Type | Description |
---|---|
Spline
|
New spline fit to given coordinates. |
Source code in cylindra/components/spline/_spline_base.py
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from_dict(d)
classmethod
Construct a spline model from a dictionary.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
d |
SplineInfo
|
Dictionary with keys "t", "c", "k", "u" and "lims". |
required |
Returns:
Type | Description |
---|---|
Spline
|
Spline object constructed from the dictionary. |
Source code in cylindra/components/spline/_spline_base.py
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get_rotator(positions=None, inverse=False)
Calculate list of Affine transformation matrix along spline, which correspond to the orientation of spline curve.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
positions |
(array - like, (N))
|
Positions. Between 0 and 1. |
None
|
inverse |
bool
|
If True, rotation matrix will be inversed. |
False
|
Returns:
Type | Description |
---|---|
Rotation
|
Rotation object at each anchor. |
Source code in cylindra/components/spline/_spline_base.py
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has_props()
True if there are any properties.
Source code in cylindra/components/spline/_spline_base.py
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invert()
Invert the direction of spline.
Returns:
Type | Description |
---|---|
Spline
|
Inverted object |
Source code in cylindra/components/spline/_spline_base.py
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is_inverted()
Return true if spline is inverted.
Source code in cylindra/components/spline/_spline_base.py
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length(start=0, stop=1, nknots=512)
Approximate the length of B-spline between [start, stop] by partitioning the spline with 'nknots' knots. nknots=256 is large enough for most cases.
Source code in cylindra/components/spline/_spline_base.py
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line(start, end)
classmethod
Create a line spline.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
start |
array_like
|
Start point of the line. |
required |
end |
array_like
|
End point of the line. |
required |
Returns:
Type | Description |
---|---|
Spline
|
Line spline. |
Source code in cylindra/components/spline/_spline_base.py
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local_cartesian(shape, depth, u=None, scale=1.0)
Generate local Cartesian coordinate systems.
The generated array can be used for ndi.map_coordinates
. The result coordinate
systems are flat, i.e., not distorted by the curvature of spline.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
shape |
(float, float)
|
Vertical and horizontal length of Cartesian coordinates. Corresponds to zx axes. |
required |
depth |
float
|
Length of y axis in nm. |
required |
u |
float
|
Position on the spline at which local Cartesian coordinates will be built. |
None
|
scale |
nm
|
Scale of coordinates, i.e. spacing of the grid. |
1.0
|
Returns:
Type | Description |
---|---|
ndarray
|
(D, V, S, H) shape. Each cooresponds to dimensional vertical, longitudinal
and horizontal axis, which is ready to be used in |
Source code in cylindra/components/spline/_spline_base.py
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local_cylindrical(r_range, depth, u=None, scale=1.0)
Generate local cylindrical coordinate systems.
The generated array can be used for ndi.map_coordinates
. The result coordinate
systems are flat, i.e., not distorted by the curvature of spline.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
r_range |
(float, float)
|
Lower and upper bound of radius in nm. |
required |
depth |
nm
|
Length of y axis in nm. |
required |
u |
float
|
Position on the spline at which local cylindrical coordinates will be built. |
None
|
scale |
nm
|
Scale of coordinates, i.e. spacing of the grid. |
1.0
|
Returns:
Type | Description |
---|---|
ndarray
|
(D, V, S, H) shape. Each cooresponds to dimensional, radius, longitudinal
and angle axis, which is ready to be used in |
Source code in cylindra/components/spline/_spline_base.py
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make_anchors(interval=None, n=None, max_interval=None)
Make anchor points at constant intervals. Either interval, number of anchor or the maximum interval between anchors can be specified.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
interval |
nm
|
Interval between anchor points. |
None
|
n |
int
|
Number of anchor points, including both ends. |
None
|
max_interval |
nm | None
|
Spline will be split by as little anchors as possible but interval between anchors will not be larger than this. The number of anchors are also guaranteed to be larger than spline order. |
None
|
Source code in cylindra/components/spline/_spline_base.py
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map(positions=None, der=0)
Calculate coordinates (or n-th derivative) at points on the spline.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
positions |
ndarray or float
|
Positions. Between 0 and 1. If not given, anchors are used instead. |
None
|
der |
int
|
|
0
|
Returns:
Type | Description |
---|---|
ndarray
|
Positions or vectors in (3,) or (N, 3) shape. |
Source code in cylindra/components/spline/_spline_base.py
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partition(n, der=0)
Return the n-partitioning coordinates of the spline.
Source code in cylindra/components/spline/_spline_base.py
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resample(max_interval=1.0, err_max=0.1)
Resample a new spline along the original spline.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
max_interval |
nm
|
Maximum interval between resampling points. |
1.0
|
err_max |
float
|
Spline fitting maximum error. |
0.1
|
Returns:
Type | Description |
---|---|
Spline
|
Resampled spline object. |
Source code in cylindra/components/spline/_spline_base.py
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|
restore()
Restore the original, not-clipped spline.
Returns:
Type | Description |
---|---|
Spline
|
Copy of the original spline. |
Source code in cylindra/components/spline/_spline_base.py
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|
shift(positions=None, shifts=None, *, err_max=1.0)
Fit spline model using a list of shifts in XZ-plane.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
positions |
sequence of float
|
Positions. Between 0 and 1. If not given, anchors are used instead. |
None
|
shifts |
ndarray
|
Shift from center in nm. Must be (N, 2). |
None
|
err_max |
float
|
Error allowed for fitting. See |
1.0
|
Returns:
Type | Description |
---|---|
Spline
|
Spline shifted by fitting to given coordinates. |
Source code in cylindra/components/spline/_spline_base.py
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|
to_dict()
Convert spline info into a dict.
Source code in cylindra/components/spline/_spline_base.py
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|
translate(shift)
Translate the spline by given shift vectors.
Source code in cylindra/components/spline/_spline_base.py
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|
with_config(config, copy_props=False)
Return a copy of the spline with a new config.
Source code in cylindra/components/spline/_spline_base.py
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|
with_extrapolation(extrapolate)
Return a copy of the spline with a new extrapolation mode.
Source code in cylindra/components/spline/_spline_base.py
114 115 116 117 118 |
|
y_to_position(y, nknots=512)
Convert y-coordinate to spline position parameter.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
y |
array - like
|
Y coordinates. |
required |
nknots |
int
|
Number of knots. Increasing the number of knots will increase the accuracy. |
512
|
Source code in cylindra/components/spline/_spline_base.py
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|
SplineConfig
dataclass
Class for spline configuration.
Source code in cylindra/components/spline/_config.py
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|
construct(**kwargs)
classmethod
Construct a SplineConfig with argument check.
Source code in cylindra/components/spline/_config.py
120 121 122 123 |
|
CylTomogram
Bases: Tomogram
Tomogram with cylindrical splines.
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
splines: SplineList
property
List of splines.
add_spline(coords, *, order=3, err_max=0.5, extrapolate=ExtrapolationMode.linear, config={})
Add spline path to tomogram.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
coords |
array - like
|
(N, 3) array of coordinates. A spline curve that fit it well is added. |
required |
order |
int
|
Order of spline curve. |
3
|
extrapolate |
str
|
Extrapolation mode of the spline. |
linear
|
config |
SplineConfig or dict
|
Configuration for spline fitting. |
{}
|
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
align_to_polarity(orientation=Ori.MinusToPlus)
Align all the splines in the direction parallel to the given polarity.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
orientation |
Ori or str
|
To which direction splines will be aligned. |
Ori.MinusToPlus
|
Returns:
Type | Description |
---|---|
Tomogram object
|
Same object with updated splines. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 |
|
fit(i=None, *, max_interval=30.0, degree_precision=0.5, binsize=1, err_max=1.0, edge_sigma=2.0, max_shift=5.0, n_rotations=5)
Roughly fit splines to cylindrical structures.
Subtomograms will be sampled at every max_interval
nm. In dense mode,
Subtomograms will be masked relative to XY-plane, using sigmoid function.
Sharpness of the sigmoid function is determined by dense_mode_sigma
(dense_mode_sigma=0
corresponds to a step function).
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to fit. |
None
|
max_interval |
nm
|
Maximum interval of sampling points in nm unit. |
30.0
|
degree_precision |
float
|
Precision of xy-tilt degree in angular correlation. |
0.5
|
binsize |
int
|
Multiscale bin size used for fitting. |
1
|
edge_sigma |
nm
|
Sharpness of mask at the edges. If not None, fitting will be executed after regions outside the cylinder are masked. Soft mask is important for precision because sharp changes in intensity cause strong correlation at the edges. |
2.0
|
max_shift |
nm
|
Maximum shift from the true center of the cylinder. This parameter is used in phase cross correlation. |
5.0
|
n_rotations |
int
|
Number of rotations to be tested during finding the cylinder center. |
5
|
Returns:
Type | Description |
---|---|
FitResult
|
Result of fitting. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
get_cylinder_model(i, offsets=(0.0, 0.0), **kwargs)
Return the cylinder model at the given spline ID.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int
|
Spline ID from which model will be created. |
required |
offsets |
tuple of float
|
Offset of the model. See :meth: |
(0.0, 0.0)
|
Returns:
Type | Description |
---|---|
CylinderModel
|
The cylinder model. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
global_cft(i=None, binsize=1)
Calculate global cylindrical fast Fourier tranformation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to analyze. |
None
|
binsize |
int
|
Multiscale bin size used for calculation. |
1
|
Returns:
Type | Description |
---|---|
ImgArray
|
Complex image. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
global_cft_params(*, i=None, binsize=1, nsamples=8, update=True)
Calculate global lattice parameters.
This function transforms tomogram using cylindrical coordinate system along
spline. This function calls straighten
beforehand, so that Fourier space is
distorted if the cylindrical structure is curved.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to analyze. |
None
|
binsize |
int
|
Multiscale bin size used for calculation. |
1
|
nsamples |
int
|
Number of cylindrical coordinate samplings for Fourier transformation.
Multiple samplings are needed because up-sampled discrete Fourier
transformation does not return exactly the same power spectra with shifted
inputs, unlike FFT. Larger |
8
|
update |
bool
|
If True, spline properties will be updated. |
True
|
Returns:
Type | Description |
---|---|
DataFrame
|
Global properties. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
global_cps(*, i=None, binsize=1)
Calculate global cylindrical power spectra.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to analyze. |
None
|
binsize |
int
|
Multiscale bin size used for calculation. |
1
|
Returns:
Type | Description |
---|---|
ImgArray
|
Complex image. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
infer_polarity(i=None, *, binsize=1, depth=40, mask_freq=True, update=True)
Infer spline polarities using polar 2D image.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to analyze. |
None
|
binsize |
int
|
Multiscale bin size used for calculation. |
1
|
depth |
nm
|
Depth of images used to infer polarities. |
40.0
|
Returns:
Type | Description |
---|---|
Ori
|
Orientation of corresponding splines. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
local_cft(*, i=None, depth=50.0, pos=None, binsize=1)
Calculate non-upsampled local cylindric Fourier transormation along spline.
This function does not up-sample.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to analyze. |
None
|
depth |
nm
|
Length of subtomogram for calculation of local parameters. |
50.0
|
pos |
int
|
Only calculate at |
None
|
binsize |
int
|
Multiscale bin size used for calculation. |
1
|
Returns:
Type | Description |
---|---|
ImgArray
|
FT images stacked along "p" axis. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
local_cft_params(*, i=None, depth=50.0, binsize=1, radius='global', nsamples=8, update=True, update_glob=False)
Calculate local lattice parameters from cylindrical Fourier space.
To determine the peaks upsampled discrete Fourier transformation is used for every subtomogram.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to analyze. |
None
|
depth |
nm
|
Length of subtomogram for calculation of local parameters. |
50.0
|
binsize |
int
|
Multiscale bin size used for calculation. |
1
|
radius |
str
|
If "local", use the local radius for the analysis. If "global", use the global radius. If a float, use the given radius. |
"global"
|
nsamples |
int
|
Number of cylindrical coordinate samplings for Fourier transformation. Multiple
samplings are needed because up-sampled discrete Fourier transformation does not
return exactly the same power spectra with shifted inputs, unlike FFT. Larger
|
8
|
update |
bool
|
If True, spline properties will be updated. |
True
|
update_glob |
bool
|
If True, global properties will be updated using the mean or mode of the local properties. |
False
|
Returns:
Type | Description |
---|---|
DataFrame
|
Local properties. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
local_cps(*, i=None, depth=50.0, pos=None, binsize=1)
Calculate non-upsampled local cylindric power spectra along spline.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to analyze. |
None
|
depth |
nm
|
Length of subtomogram for calculation of local parameters. |
50.0
|
pos |
int
|
Only calculate at |
None
|
binsize |
int
|
Multiscale bin size used for calculation. |
1
|
Returns:
Type | Description |
---|---|
ImgArray
|
FT images stacked along "p" axis. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
local_radii(*, i=None, depth=50.0, binsize=1, min_radius=1.0, max_radius=100.0, update=True, update_glob=True)
Measure the local radii along the splines.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to analyze. |
None
|
depth |
nm
|
Longitudinal length of subtomograms for calculation. |
50.0
|
binsize |
int
|
Multiscale binsize to be used. |
1
|
min_radius |
nm
|
Minimum radius of the cylinder. |
1.0
|
max_radius |
nm
|
Maximum radius of the cylinder. |
100.0
|
update |
bool
|
If True, spline properties will be updated. |
True
|
update_glob |
bool
|
If True, global properties will be updated using the mean of the local radii. |
True
|
Returns:
Type | Description |
---|---|
Series
|
Radii along the spline. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
make_anchors(i=None, *, interval=None, n=None, max_interval=None)
Make anchors on spline object(s).
Parameters:
Name | Type | Description | Default |
---|---|---|---|
interval |
nm
|
Anchor intervals. |
None
|
n |
int
|
Number of anchors |
None
|
max_interval |
nm
|
Maximum interval between anchors. |
None
|
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
map_centers(i=None, *, interval=1.0, orientation=None, rotate_molecules=True)
Mapping molecules along the center of a cylinder.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that mapping will be calculated. |
None
|
interval |
float(nm)
|
Interval of molecules. |
1.0
|
rotate_molecules |
bool
|
If True, twist the molecule orientations according to the spline twist. |
True
|
Returns:
Type | Description |
---|---|
Molecules
|
Molecules object with mapped coordinates and angles. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
map_monomers(i=None, *, offsets=None, orientation=None, extensions=(0, 0), **kwargs)
Map monomers in a regular cylinder shape.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that mapping will be calculated. |
None
|
offsets |
tuple of float
|
The offset of origin of oblique coordinate system to map monomers. |
None
|
orientation |
Ori or str
|
Orientation of the y-axis of each molecule. |
None
|
Returns:
Type | Description |
---|---|
Molecules
|
Object that represents monomer positions and angles. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
map_on_grid(i=None, coords=(), *, offsets=None, orientation=None, **kwargs)
Map monomers in a regular cylinder shape.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that mapping will be calculated. |
None
|
coords |
ndarray
|
Integer coordinates on the cylinder surface. |
()
|
offsets |
tuple of float
|
The offset of origin of oblique coordinate system to map monomers. |
None
|
orientation |
Ori or str
|
Orientation of the y-axis of each molecule. |
None
|
Returns:
Type | Description |
---|---|
Molecules
|
Object that represents monomer positions and angles. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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|
map_pf_line(i=None, *, interval=1.0, offsets=(0.0, 0.0), orientation=None)
Mapping molecules along a protofilament line.
This method is useful when you want to visualize seam or protofilament, or assign molecules for subtomogram averaging of seam binding protein or doublet microtubule.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that mapping will be calculated. |
None
|
offsets |
(float, float)
|
Axial offset in nm and angular offset in degree. |
(0.0, 0.0)
|
Returns:
Type | Description |
---|---|
Molecules
|
Object that represents protofilament positions and angles. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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measure_radius(i=None, *, binsize=1, positions='auto', min_radius=1.0, max_radius=100.0, update=True)
Measure radius using radial profile from the center.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to measure. |
None
|
binsize |
int
|
Multiscale bin size used for radius calculation. |
1
|
positions |
array - like or 'auto' or 'anchor'
|
Sampling positions (between 0 and 1) to calculate radius. If "anchor" is given, anchors of the spline will be used. If "auto" is given, three positions along the spline will be used. |
"auto"
|
min_radius |
nm
|
Minimum radius of the cylinder. |
1.0
|
max_radius |
nm
|
Maximum radius of the cylinder. |
100.0
|
update |
bool
|
If True, global radius property will be updated. |
True
|
Returns:
Type | Description |
---|---|
float(nm)
|
Cylinder radius. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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refine(i=None, *, max_interval=30.0, binsize=1, err_max=1.0, corr_allowed=0.9, max_shift=2.0, n_rotations=3)
Spline refinement using global lattice structural parameters.
Refine spline using the result of previous fit and the global structural parameters. During refinement, Y-projection of XZ cross section of cylinder is rotated with the twist angles, thus is much more precise than the coarse fitting.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to fit. |
None
|
max_interval |
nm
|
Maximum interval of sampling points in nm unit. |
24.0
|
binsize |
int
|
Multiscale bin size used for refining. |
1
|
corr_allowed |
(float, defaul is 0.9)
|
How many images will be used to make template for alignment. If 0.9, then top 90% will be used. |
0.9
|
max_shift |
nm
|
Maximum shift from the true center of the cylinder. This parameter is used in phase cross correlation. |
2.0
|
n_rotations |
int
|
Number of rotations to be tested during finding the cylinder center. |
3
|
Returns:
Type | Description |
---|---|
FitResult
|
Result of fitting. |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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straighten(i=None, *, size=None, range_=(0.0, 1.0), chunk_length=None, binsize=1)
Straightening by building curved coordinate system around splines. Currently Cartesian coordinate system and cylindrical coordinate system are supported.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to straighten. |
None
|
size |
float(nm)
|
Vertical/horizontal box size. |
None
|
range_ |
tuple[float, float]
|
Range of spline domain. |
(0.0, 1.0)
|
chunk_length |
nm
|
If spline is longer than this, it will be first split into chunks, straightened respectively and all the straightened images are concatenated afterward, to avoid loading entire image into memory. |
None
|
binsize |
int
|
Multiscale bin size used for calculation. |
1
|
Returns:
Type | Description |
---|---|
ImgArray
|
Straightened image. If Cartesian coordinate system is used, it will have "zyx". |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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straighten_cylindric(i=None, *, radii=None, range_=(0.0, 1.0), chunk_length=None, binsize=1)
Straightening by building curved coordinate system around splines. Currently Cartesian coordinate system and cylindrical coordinate system are supported.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
i |
int or iterable of int
|
Spline ID that you want to straighten. |
None
|
radii |
tuple of float (nm)
|
Lower/upper limit of radius. |
None
|
range_ |
tuple[float, float]
|
Range of spline domain. |
(0.0, 1.0)
|
chunk_length |
nm
|
If spline is longer than this, it will be first split into chunks, straightened respectively and all the straightened images are concatenated afterward, to avoid loading entire image into memory. |
None
|
binsize |
int
|
Multiscale bin size used for calculation. |
1
|
Returns:
Type | Description |
---|---|
ImgArray
|
Straightened image. If Cartesian coordinate system is used, it will have "zyx". |
Source code in cylindra/components/tomogram/_cyl_tomo.py
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Tomogram
Lazy-loading/multi-scale tomogram object.
It is always connected to a 3D image but processed lazily. Thus you can create a lot of Tomogram objects without MemoryError. Subtomograms are temporarily loaded into memory via cache map. Once memory usage exceed certain amount, the subtomogram cache will automatically deleted from the old ones.
Source code in cylindra/components/tomogram/_tomo_base.py
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|
image: ip.ImgArray | ip.LazyImgArray
property
Tomogram image data.
is_dummy: bool
property
True if this tomogram object does not have a real image.
is_inverted: bool
property
True if this image is inverted
metadata: dict[str, Any]
property
writable
Metadata relevant to the tomogram.
multiscaled: list[tuple[int, ip.ImgArray]]
property
Get all multi-scale factor and the corresponding multiscaled images.
scale: nm
property
Scale of the tomogram.
source: Path
property
Path to the source file.
tilt: dict[str, Any]
property
Tilt model as a dictionary.
tilt_model
property
Tilt model of the tomogram.
__hash__()
Use unsafe hash.
Source code in cylindra/components/tomogram/_tomo_base.py
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add_multiscale(binsize, compute=True)
Add new multiscaled image of given binsize.
Source code in cylindra/components/tomogram/_tomo_base.py
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dummy(*, scale=1.0, tilt=None, binsize=(), source=None, shape=(24, 24, 24), name=None)
classmethod
Create a dummy tomogram.
Source code in cylindra/components/tomogram/_tomo_base.py
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from_image(img, *, scale=None, tilt=None, binsize=(), compute=True)
classmethod
Construct a Tomogram object from a image array.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
img |
array - like
|
Input image. |
required |
scale |
float
|
Pixel size in nm. If not given, will try to read from image header. |
None
|
tilt |
tuple of float
|
Tilt model. |
None
|
binsize |
int or iterable of int
|
Binsize to generate multiscale images. If not given, will not generate. |
()
|
compute |
bool
|
Whether to compute the binned images. |
True
|
Returns:
Type | Description |
---|---|
Tomogram
|
Tomogram object with the image that has just been read and multi-scales. |
Source code in cylindra/components/tomogram/_tomo_base.py
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get_multiscale(binsize, add=False)
Get multiscaled image of given binsize.
Source code in cylindra/components/tomogram/_tomo_base.py
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get_subtomogram_loader(mole, output_shape=None, binsize=1, order=1)
Create a subtomogram loader from molecules.
Source code in cylindra/components/tomogram/_tomo_base.py
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imread(path, *, scale=None, tilt=None, binsize=(), eager=False, compute=True)
classmethod
Read a image as a dask array.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
path |
path - like
|
Path to the image file. |
required |
scale |
float
|
Pixel size in nm. If not given, will try to read from image header. |
None
|
tilt |
tuple of float
|
Tilt model. |
None
|
binsize |
int or iterable of int
|
Binsize to generate multiscale images. If not given, will not generate. |
()
|
eager |
bool
|
Whether to read the image lazily. If True, the entire image will be read into the memory. |
False
|
Returns:
Type | Description |
---|---|
Tomogram
|
Tomogram object with the image that has just been read and multi-scales. |
Source code in cylindra/components/tomogram/_tomo_base.py
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invert(cache=False)
Invert tomogram intensities in-place.
Source code in cylindra/components/tomogram/_tomo_base.py
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multiscale_translation(binsize)
Get lateral translation of binned image in nm.
Source code in cylindra/components/tomogram/_tomo_base.py
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nm2pixel(value, binsize=1)
Convert nm float value into pixel value. Useful for conversion from coordinate to pixel position.
Returns:
Type | Description |
---|---|
ndarray or int
|
Pixel position. |
Source code in cylindra/components/tomogram/_tomo_base.py
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BaseComponent
Base class for all tomographic components.
Source code in cylindra/components/_base.py
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from_dict(js)
Construct a component from a dictionary.
Source code in cylindra/components/_base.py
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from_json(file_path)
classmethod
Construct a spline model from a json file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
file_path |
str
|
Path to json file. |
required |
Returns:
Type | Description |
---|---|
BaseComponent
|
Object constructed from the json file. |
Source code in cylindra/components/_base.py
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to_dict()
abstractmethod
Convert a component to a dictionary.
Source code in cylindra/components/_base.py
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to_json(file_path, *, cls=None)
Save the model in a json format.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
file_path |
str
|
Path to the file. |
required |
cls |
JSONEncoder
|
Custom JSON encoder, by default None |
None
|
Source code in cylindra/components/_base.py
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AnnealingResult
dataclass
Dataclass for storing the annealing results.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
energies |
ndarray
|
History of energies of the annealing process. |
required |
batch_size |
int
|
Batch size used in the annealing process. |
required |
time_const |
float
|
Time constant used for cooling. |
required |
indices |
ndarray
|
The optimized indices of the molecules. |
required |
niter |
int
|
Number of iterations. |
required |
state |
str
|
Optimization state. |
required |
Source code in cylindra/components/landscape.py
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Landscape
dataclass
Energy landscape array.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
energies |
NDArray[float32]
|
4D array of energy values. |
required |
molecules |
Molecules
|
Molecules object. |
required |
argmax |
NDArray[int32]
|
Argmax indices to track which rotation resulted in the best alignment. |
required |
quaternions |
NDArray[float32]
|
Quaternions used for template rotation. |
required |
scale_factor |
float
|
Scale factor to convert from pixels to nanometers (upsampling considered).
|
required |
Source code in cylindra/components/landscape.py
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|
offset: NDArray[np.int32]
property
Shift from the corner (0, 0, 0) to the center.
offset_nm: NDArray[np.float32]
property
Offset in nm.
__getitem__(key)
Subset of the landscape.
Source code in cylindra/components/landscape.py
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annealing_model(spl, distance_range_long, distance_range_lat, angle_max=None, temperature_time_const=1.0, temperature=None, cooling_rate=None, reject_limit=None)
Get an annealing model using the landscape.
Source code in cylindra/components/landscape.py
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create_surface(level=None, resolution=None, show_min=True)
Create a isosurface data from the landscape
Source code in cylindra/components/landscape.py
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from_dir(path)
classmethod
Load a landscape from a directory.
Source code in cylindra/components/landscape.py
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|
from_loader(loader, template, mask=None, max_shifts=(0.8, 0.8, 0.8), upsample_factor=5, alignment_model=alignment.ZNCCAlignment)
classmethod
Construct a landscape from a loader object.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
loader |
LoaderBase
|
Any loader object from |
required |
template |
template input type
|
Template image or a list of template images to be used. |
required |
mask |
mask input type
|
Mask image to be used, by default None |
None
|
max_shifts |
(float, float, float)
|
Maximum shifts in nm, in (Z, Y, X) order. |
(0.8, 0.8, 0.8)
|
upsample_factor |
int
|
Upsampling factor for landscape construction. |
5
|
alignment_model |
alignment model object
|
Alignment model to be used to evaluate correlation score. |
ZNCCAlignment
|
Source code in cylindra/components/landscape.py
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|
normed(sd=True)
Return a landscape with normalized mean energy.
Source code in cylindra/components/landscape.py
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run_annealing(spl, distance_range_long, distance_range_lat, angle_max=None, temperature_time_const=1.0, temperature=None, cooling_rate=None, reject_limit=None, random_seeds=[0])
Run simulated mesh annealing.
Source code in cylindra/components/landscape.py
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run_min_energy(spl=None)
Minimize energy for each local landscape independently.
Source code in cylindra/components/landscape.py
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run_viterbi(dist_range, angle_max=None)
Run Viterbi alignment.
Source code in cylindra/components/landscape.py
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run_viterbi_fixed_start(first, range_long=(4.0, 4.28), angle_max=5.0)
Run Viterbi alignment with a fixed start edge.
Source code in cylindra/components/landscape.py
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save(path)
Save the landscape to a directory.
Source code in cylindra/components/landscape.py
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transform_molecules(molecules, indices, detect_peak=False)
Transform the input molecules based on the landscape.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
molecules |
Molecules
|
Molecules object to be transformed. |
required |
indices |
integer array
|
Indices in the landscape to be used for transformation. |
required |
detect_peak |
bool
|
If True, landscape will be sub-sampled to detect the peak in higher precision. This should be false for constrained alignment, as the detected peak usually does not represent the optimal result. |
False
|
Returns:
Type | Description |
---|---|
Molecules
|
Transformed molecules. |
Source code in cylindra/components/landscape.py
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SurfaceData
Tuple for storing isosurface data for landscapes.
Source code in cylindra/components/landscape.py
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ViterbiResult
dataclass
Dataclass for storing the Viterbi alignment results.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
indices |
ndarray
|
The optimized indices of the molecules. |
required |
score |
float
|
The score of the optimal alignment. |
required |
Source code in cylindra/components/landscape.py
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delayed_isosurface(arr, level, spacing, step_size=1)
Create an isosurface from a 3D array using marching cubes algorithm.
Source code in cylindra/components/landscape.py
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CorrelationSeamSearcher
Seam searcher based on correlation with the template.
Source code in cylindra/components/seam_search.py
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SeamSearcher
Source code in cylindra/components/seam_search.py
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search(*args, **kwargs)
abstractmethod
Search for the seam position.
Source code in cylindra/components/seam_search.py
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|