PackedCylinders¶
from mcot.dippi.geometry.cylinders import PackedCylinders
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class
mcot.dippi.geometry.cylinders.PackedCylinders(gratios=0.7, angles=(0.0, 1.5707963267948966), b0=(0, 1, 0), radius=0.5, spacing=1.0, chi_iso=- 1e-07, chi_aniso=- 1e-07)[source]¶ Models regularly packed cylinders with varying g-ratio’s and orientations
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__init__(gratios=0.7, angles=(0.0, 1.5707963267948966), b0=(0, 1, 0), radius=0.5, spacing=1.0, chi_iso=- 1e-07, chi_aniso=- 1e-07)[source]¶ Defines a set of packed cylinders
- Parameters
gratios – 2D array with sequence of g-ratio (first dimension is misaligned with angles, second dimension is the same along which angles vary, i.e. y-axis).
angles – Angle of axons around the y-axis for fibres stacked above each other in y-axis (0 means pointing in z-direction)
b0 – vector with the main magnetic field orientation
radius – radius of the axons
spacing – spacing between the axon centres
chi_iso – isotropic susceptibility of the myelin
chi_aniso – anisotropic susceptibility of the myelin
Inheritance diagram
Methods
external_phase(npoints[, maxrepeat])Computes the phase due to the contributions of any axons outside of the periodic block
in_axon(positions)Computes which spins are inside the axons
recompute_external_phase([npoints, maxrepeat])Computes and sets the phase due to external axons
Attributes
n_repeat-
external_phase¶
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PackedCylinders.external_phase(npoints, maxrepeat=50)[source]¶ Computes the phase due to the contributions of any axons outside of the periodic block
- Parameters
npoints – density of point per spacing (in 1D)
maxrepeat – maximum number of repeats
- Returns
(n_repeat[1], n_repeat[0] * npoints, n_repeat[1] * npoints) array with the phase