plenoptomos.unsupported package

Submodules

plenoptomos.unsupported.geometry module

Created on Thu Sep 13 18:07:48 2018

@author: Nicola VIGANÒ, Computational Imaging group, CWI, The Netherlands, and ESRF - The European Synchrotron, Grenoble, France

class plenoptomos.unsupported.geometry.GeometryTransformation(t=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]], dtype=float32), s=array([0., 0., 0.], dtype=float32))

Bases: object

Geometry transformation class. It allows to manipulate position and direction vectors.

apply_direction(vec)

Implements application of the transformation to a direction vector.

Parameters

vec (numpy.array_like) – Direction vector

Returns

Result of the transformation

Return type

numpy.array_like

apply_position(vec)

Implements application of the transformation to a position vector.

Parameters

vec (numpy.array_like) – Position vector

Returns

Result of the transformation

Return type

numpy.array_like

static get_axis_angle(vec_ref, vec_dir)

Computes the rotation axis and angle of the rotation that transformed vec_ref into vec_dir.

Parameters

• vec_ref (numpy.array_like) – The initial vector.

• vec_dir (numpy.array_like) – The result vector.

Returns

The normalized rotation axis and angle.

Return type

tuple(numpy.array_like, float)

static get_rotation_components(rot_axis)

Computes the rotation components for the given rotation axis.

Parameters

rot_axis (<3, > numpy.array_like) – The rotation axis.

Returns

The rotation components

Return type

tuple(<3, 3> numpy.array_like, <3, 3> numpy.array_like, <3, 3> numpy.array_like)

static get_rotation_matrix(rotcomp, angle)

Computes the rotation matrix for the given rotation components and angle.

Parameters

• rotcomp (tuple(<3, 3> numpy.array_like, <3, 3> numpy.array_like, <3, 3> numpy.array_like)) – The rotation components, computed with get_rotation_components

• angle (float) – The rotation angle

Returns

The rotation matrix

Return type

<3, 3> numpy.array_like

static get_rototranslation(axis, angles, axis_origin=None)

Create a roto-translation transformation.

Parameters

• axis (numpy.array_like) – Rotation axis

• angles (float) – rotation angle

• axis_origin (numpy.array_like, optional. Default: None) – Origin of the rotation axis

Returns

The roto-translation transformation

Return type

GeometryTransformation

static get_scale(scale)

Creates a scaling transformation.

Parameters

scale (float) – The scaling factor.

Returns

The scaling transformation

Return type

GeometryTransformation

static get_transform(t_type, *args, **keywords)

Creates a transformation.

Parameters

t_type (string) – Type of transformation. Options are: ‘rot’ | ‘tr’

Returns

The chosen transformation

Return type

GeometryTransofrm

static get_translation(point)

Create a transflation transformation.

Parameters

point (numpy.array_like) – Translation position.

Returns

The translation transformation

Return type

GeometryTransformation

rmatvec(vec)

Implement the transpose of the transformation to vector operation.

Parameters

vec (numpy.array_like <3, > or <4, >) – Direction vectors.

plenoptomos.unsupported.reconstruction module

Created on Wed Mar 6 12:20:48 2019

@author: Nicola VIGANÒ, Computational Imaging group, CWI, The Netherlands, and ESRF - The European Synchrotron, Grenoble, France

class plenoptomos.unsupported.reconstruction.Reconstruct3D(vol_geom, proj_geom, super_sampling=1, gpu_index=None)

Bases: object

bp(data)

cp(data, iterations=100, pars={})

fp(vol)

reconstruct(data, algo='SIRT3D_CUDA', iterations=25, pars={})

sirt(data, iterations=25, pars={})

plenoptomos.unsupported.reconstruction.correct_projs(projs, flats, darks, crop=None, pad=None)

plenoptomos.unsupported.reconstruction.get_geometry(dset_path, projs_shape, beam_geometry='cone', vol_shift_mm=0.0, vol_size_add=None, detector_tilt_deg=None)

plenoptomos.unsupported.reconstruction.get_scanner_conf(dset_path)

plenoptomos.unsupported.reconstruction.load_images(dset_path, imprefix)

plenoptomos.unsupported.testing module

Created on Mon Jun 18 16:51:41 2018

@author: Nicola VIGANÒ, Computational Imaging group, CWI, The Netherlands, and ESRF - The European Synchrotron, Grenoble, France

class plenoptomos.unsupported.testing.Blurring(cameras, verbose=False)

Bases: object

blur(lfs, coordinates='vu')

create_psf_lenses(coordinates='vu', airy_rings=3, refocus_distance=None, up_sampling=1, plot_psfs=False, use_otf=False)

class plenoptomos.unsupported.testing.Tester(test_name, lfs, test_params={}, rec_params={}, test_conds={}, is_rgb=False, result_dir=None, save=True)

Bases: object

default_conditions = {'down_sampling_st': 1, 'down_sampling_uv': 1, 'extras': ''}

default_rec_params = {'border': 8, 'data_term': 'l2', 'fourier_method': 'slice', 'iterations': 50, 'psf': None, 'up_sampling_function': 'flat', 'up_sampling_st': 1}

default_test_params = {'algo': [], 'beam': [], 'domain': [], 'lambda_reg': [], 'zs': []}

get_options_number()

get_test_option(option_name, ind, struct=None)

launch_reconstruction(ii_t)

plenoptomos.unsupported.utils_img module

Created on Fri Dec 8 15:24:12 2017

@author: Nicola VIGANÒ, Computational Imaging group, CWI, The Netherlands, and ESRF - The European Synchrotron, Grenoble, France

class plenoptomos.unsupported.utils_img.MovieCreator(out_dir, lf, z0s, focal_stack, dmap, all_focus, use_overlay=True)

Bases: object

create_allfocus_frames(num_frames=1)

create_dmap_frames(num_frames=1)

create_refocus_frame(z_ind)

create_simple_frame(img)

create_static_frames(num_frames)

create_sublf_frame(sublf_size, sublf_center_vu=None)

create_transition(from_img, to_img, num_frames)

create_transition_frame(from_img, to_img, percentage)

create_transition_sublf(final_sublf_size, direction='to')

overlay_text_on_image(img_ref, img_text)

render_distance(img_size, z)

render_text(img_size, t)

to_01(img)

class plenoptomos.unsupported.utils_img.ShiftsFinderVolume3D(data_fix, data_move, do_clear=True, clims=None)

Bases: object

ax_lr = [2, 2, 1]

ax_ud = [1, 0, 0]

axs_rot = ['Z', 'Y', 'X']

planes_vis = ['XY', 'XZ', 'YZ']

show(*args, **kwords)

update(direction)

update_ax(ax, data)

Module contents

Unsupported utility tools.

@author: Nicola VIGANÒ, Computational Imaging group, CWI, The Netherlands, and ESRF - The European Synchrotron, Grenoble, France

Created on Mon Jun 8 15:28:00 2020