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nabu.resources.helical_calc

source module nabu.resources.helical_calc

Module for calculations of helical scans

Classes

Functions

source get_angular_precision(angles_deg, percentile=1)

Return the angular precision, in degrees of an array of angles Angles are assumed to be a monotonic sequence, possibly wrapped (eg. to pi or 2pi).

source class HelicalScanCalc(dataset_info, dz=None, all_angles=None)

Methods

  • height — Get the "heights" (in pixels) for a given z-slice, as a function of angular indices. Ideally: h(z, i) = z + i*dz

  • get_angular_indices

  • i_min — Return the first angular index where "z" enters the field of view

  • i_max — Return the last angular index where "z" enters the field of view

  • get_z_indices

  • z_min — Return the minimum "z" that enters the FoV starting from angular index "i"

  • z_max — Return the maximum "z" that exits the FoV at angular index "i"

  • get_angles — Get angles associated to "z", i.e, get all the angles for which the sample at height "z" is imaged.

  • compute_angles_weights — Compute the "weights" to be applied at each angle for a given z-sinogram. When doing a helical tomography, some angles are imaged more than others. This function counts how many times each angle of a given z-sinogram is seen.

  • get_number_of_steps — Return the number of steps to reconstruct the whole scan, i.e maximum k such that k * chunk_size < n_angles - 1 and (k+1)*chunk_size >= n_angles - 1

source method HelicalScanCalc.height(z, i)

Get the "heights" (in pixels) for a given z-slice, as a function of angular indices. Ideally: h(z, i) = z + i*dz

source method HelicalScanCalc.get_angular_indices(z)

Get the indices corresponding to angles where a given "z" is imaged

angular_indices(z) = {i, h(z, i) is in FoV}

source method HelicalScanCalc.i_min(z)

Return the first angular index where "z" enters the field of view

source method HelicalScanCalc.i_max(z)

Return the last angular index where "z" enters the field of view

source method HelicalScanCalc.get_z_indices(i)

Get the z-indices corresponding to slices that are in the FoV at angular index "i"

z_indices(i) = {z, h(z, i) is in FoV}

source method HelicalScanCalc.z_min(i)

Return the minimum "z" that enters the FoV starting from angular index "i"

source method HelicalScanCalc.z_max(i)

Return the maximum "z" that exits the FoV at angular index "i"

source method HelicalScanCalc.get_angles(z)

Get angles associated to "z", i.e, get all the angles for which the sample at height "z" is imaged.

source method HelicalScanCalc.compute_angles_weights(z, angles=None, tol=None)

Compute the "weights" to be applied at each angle for a given z-sinogram. When doing a helical tomography, some angles are imaged more than others. This function counts how many times each angle of a given z-sinogram is seen.

source method HelicalScanCalc.get_number_of_steps(chunk_size)

Return the number of steps to reconstruct the whole scan, i.e maximum k such that k * chunk_size < n_angles - 1 and (k+1)*chunk_size >= n_angles - 1

source get_extraction_points(z1, z2, helical_calc, angles_chunk_size=1000)

source get_memory_footprint(helical_calculator, start_z, end_z, angles_chunk_size=1000, rec_shape=None)

Return the memory footprint in GB (not GiB !) for various components

end_z is included!