Index

A

acryo module acryo.alignment module acryo.backend module acryo.classification module acryo.classification.pca module acryo.loader module acryo.molecules module acryo.molecules.core module acryo.pick module acryo.pipe module acryo.simulator module acryo.testing module acryo.testing.core module acryo.tilt module

acryo.tilt.core module add_loader() (acryo.BatchLoader method) (acryo.loader.BatchLoader method) add_molecules() (acryo.simulator.TomogramSimulator method) (acryo.TomogramSimulator method) add_tomogram() (acryo.BatchLoader method) (acryo.loader.BatchLoader method) affine_matrix() (acryo.alignment.AlignmentResult method) (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) affine_transform() (acryo.backend.Backend method) align() (acryo.alignment.BaseAlignmentModel method) (acryo.alignment.RotationImplemented method) AlignmentResult (class in acryo.alignment) AnyArray (class in acryo.backend) append() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) apply_mask() (acryo.tilt.TiltSeriesModel method) arange() (acryo.backend.Backend method) argmax() (acryo.backend.Backend method) argmin() (acryo.backend.Backend method) array() (acryo.backend.Backend method) asarray() (acryo.backend.Backend method) asnumpy() (acryo.backend.Backend method) astype() (acryo.backend.AnyArray method) axes_to_rotator() (in module acryo.molecules)

B

Backend (class in acryo.backend) BaseAlignmentModel (class in acryo.alignment) BatchLoader (class in acryo) (class in acryo.loader)

binning() (acryo.BatchLoader method) (acryo.loader.BatchLoader method) (acryo.loader.SubtomogramLoader method) (acryo.SubtomogramLoader method) blobs() (in module acryo.testing)

C

center_by_mass() (in module acryo.pipe) closing() (in module acryo.pipe) collect_molecules() (acryo.simulator.TomogramSimulator method) (acryo.TomogramSimulator method) Component (class in acryo.simulator) components (acryo.simulator.TomogramSimulator property) (acryo.TomogramSimulator property) compose() (acryo.pipe.ImageConverter method) concat() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method) concat_with() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) conj() (acryo.backend.AnyArray method) construct_loading_tasks() (acryo.BatchLoader method) (acryo.loader.BatchLoader method) (acryo.loader.MockLoader method) (acryo.loader.SubtomogramLoader method) (acryo.MockLoader method) (acryo.SubtomogramLoader method)

convert() (acryo.pipe.ImageConverter method) converter_function() (in module acryo.pipe) copy() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) (acryo.simulator.TomogramSimulator method) (acryo.TomogramSimulator method) corner_safe (acryo.simulator.TomogramSimulator property) (acryo.TomogramSimulator property) count() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) create_mask() (acryo.tilt.NoWedge method) (acryo.tilt.SingleAxis method) (acryo.tilt.TiltSeriesModel method) (acryo.tilt.UnionAxes method) cross() (in module acryo.molecules.core) (in module acryo.simulator) cumsum() (acryo.backend.Backend method) cutby() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method)

D

dilation() (in module acryo.pipe) DoGPicker (class in acryo.pick) dot() (acryo.backend.AnyArray method) drop_features() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method)

dtype (acryo.backend.AnyArray property) dual_axis() (in module acryo.tilt) (in module acryo.tilt.core)

E

empty() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method)

euler_angle() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) exp() (acryo.backend.Backend method)

F

features (acryo.Molecules property) (acryo.molecules.core.Molecules property) (acryo.molecules.Molecules property) fftfreq() (acryo.backend.Backend method) fftn() (acryo.backend.Backend method) fftshift() (acryo.backend.Backend method) filter() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) fit() (acryo.alignment.BaseAlignmentModel method) (acryo.alignment.RotationImplemented method) fix() (acryo.backend.Backend method) from_array() (in module acryo.pipe) from_arrays() (in module acryo.pipe) from_atoms() (in module acryo.pipe) from_axes() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method) from_csv() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method) from_dataframe() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method) from_euler() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method)

from_euler_xyz_coords() (in module acryo.molecules) from_file() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method) (in module acryo.pipe) from_files() (in module acryo.pipe) from_gaussian() (in module acryo.pipe) from_loaders() (acryo.BatchLoader class method) (acryo.loader.BatchLoader class method) from_matrix() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method) from_parquet() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method) from_quat() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method) from_random() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method) from_rotvec() (acryo.Molecules class method) (acryo.molecules.core.Molecules class method) (acryo.molecules.Molecules class method) full() (acryo.backend.Backend method)

G

gaussian_filter() (in module acryo.pipe) gaussian_smooth() (in module acryo.pipe) get_bases() (acryo.classification.pca.PcaClassifier method) (acryo.classification.PcaClassifier method) get_missing_wedge_mask() (acryo.alignment.TomographyInput method) get_params_and_depth() (acryo.pick.DoGPicker method) (acryo.pick.LoGPicker method) get_tomogram() (acryo.testing.core.TomogramGenerator method) (acryo.testing.TomogramGenerator method)

get_transform() (acryo.classification.pca.PcaClassifier method) (acryo.classification.PcaClassifier method) grid_shape (acryo.testing.core.TomogramGenerator property) (acryo.testing.TomogramGenerator property) group_by() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) groupby() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method)

H

has_hetero_templates (acryo.alignment.BaseAlignmentModel property) has_rotation (acryo.alignment.BaseAlignmentModel property) (acryo.alignment.RotationImplemented property)

head() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) highpass_filter() (in module acryo.pipe)

I

ifftn() (acryo.backend.Backend method) ifftshift() (acryo.backend.Backend method) imag (acryo.backend.AnyArray property) image (acryo.loader.SubtomogramLoader property) (acryo.simulator.Component attribute) (acryo.SubtomogramLoader property) ImageConverter (class in acryo.pipe) ImageProvider (class in acryo.pipe)

images (acryo.BatchLoader property) (acryo.loader.BatchLoader property) imread() (acryo.loader.SubtomogramLoader class method) (acryo.SubtomogramLoader class method) (in module acryo) indices() (acryo.backend.Backend method) input_shape (acryo.alignment.BaseAlignmentModel property) irfftn() (acryo.backend.Backend method) is_multi_templates (acryo.alignment.BaseAlignmentModel property)

K

kmeans (acryo.classification.pca.PcaClassifier property) (acryo.classification.PcaClassifier property)

L

label (acryo.alignment.AlignmentResult attribute) labels (acryo.classification.pca.PcaClassifier property) (acryo.classification.PcaClassifier property) landscape() (acryo.alignment.BaseAlignmentModel method) linear_transform() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) loaders (acryo.BatchLoader property) (acryo.loader.BatchLoader property)

local_coordinates() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) LoGPicker (class in acryo.pick) lowpass_filter() (acryo.backend.Backend method) (in module acryo.pipe) lowpass_filter_ft() (acryo.backend.Backend method)

M

map_coordinates() (acryo.backend.Backend method) mask (acryo.alignment.BaseAlignmentModel property) mask_missing_wedge() (acryo.alignment.TomographyInput method) masked_difference() (acryo.alignment.TomographyInput method) matrix() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) max() (acryo.backend.Backend method) maycopy() (acryo.backend.Backend method) mean() (acryo.backend.AnyArray method) (acryo.backend.Backend method) meshgrid() (acryo.backend.Backend method) min() (acryo.backend.Backend method) missing_wedge_mask() (acryo.backend.Backend method) MockLoader (class in acryo) (class in acryo.loader) module acryo acryo.alignment acryo.backend acryo.classification acryo.classification.pca acryo.loader acryo.molecules acryo.molecules.core acryo.pick acryo.pipe acryo.simulator acryo.testing acryo.testing.core acryo.tilt acryo.tilt.core

molecules (acryo.BatchLoader property) (acryo.loader.BatchLoader property) (acryo.loader.MockLoader property) (acryo.loader.SubtomogramLoader property) (acryo.MockLoader property) (acryo.simulator.Component attribute) (acryo.SubtomogramLoader property) Molecules (class in acryo) (class in acryo.molecules) (class in acryo.molecules.core)

N

name (acryo.backend.Backend property) ndim (acryo.backend.AnyArray property) niter (acryo.alignment.BaseAlignmentModel property) (acryo.alignment.RotationImplemented property)

no_wedge() (in module acryo.tilt) (in module acryo.tilt.core) noise_sigma (acryo.testing.core.TomogramGenerator property) (acryo.testing.TomogramGenerator property) NoWedge (class in acryo.tilt)

O

order (acryo.simulator.TomogramSimulator property) (acryo.TomogramSimulator property)

P

pad() (acryo.backend.Backend method) pca (acryo.classification.pca.PcaClassifier property) (acryo.classification.PcaClassifier property) PcaClassifier (class in acryo.classification) (class in acryo.classification.pca) PCCAlignment (class in acryo.alignment) percentile() (acryo.backend.Backend method) pick_in_chunk() (acryo.pick.DoGPicker method) (acryo.pick.LoGPicker method) (acryo.pick.ZNCCTemplateMatcher method) pick_molecules() (acryo.pick.ZNCCTemplateMatcher method)

plot_transform() (acryo.classification.pca.PcaClassifier method) (acryo.classification.PcaClassifier method) pos (acryo.Molecules property) (acryo.molecules.core.Molecules property) (acryo.molecules.Molecules property) pre_transform() (acryo.alignment.BaseAlignmentModel method) (acryo.alignment.TomographyInput method) predict() (acryo.classification.pca.PcaClassifier method) (acryo.classification.PcaClassifier method) provide() (acryo.pipe.ImageProvider method) provider_function() (in module acryo.pipe)

Q

quat (acryo.alignment.AlignmentResult attribute) quaternion() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method)

quaternions (acryo.testing.core.TomogramGenerator property) (acryo.testing.TomogramGenerator property)

R

real (acryo.backend.AnyArray property) replace() (acryo.BatchLoader method) (acryo.loader.BatchLoader method) (acryo.loader.MockLoader method) (acryo.loader.SubtomogramLoader method) (acryo.MockLoader method) (acryo.simulator.TomogramSimulator method) (acryo.SubtomogramLoader method) (acryo.TomogramSimulator method) rfftn() (acryo.backend.Backend method) rotate_by() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) rotate_by_euler_angle() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) rotate_by_matrix() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) rotate_by_quaternion() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method)

rotate_by_rotvec() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) rotate_by_rotvec_internal() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) rotate_random() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) rotated_crop() (acryo.backend.Backend method) RotationImplemented (class in acryo.alignment) rotator (acryo.Molecules property) (acryo.molecules.core.Molecules property) (acryo.molecules.Molecules property) rotvec() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) run() (acryo.classification.pca.PcaClassifier method) (acryo.classification.PcaClassifier method)

S

sample() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) sample_molecules() (acryo.testing.core.TomogramGenerator method) (acryo.testing.TomogramGenerator method) scale (acryo.simulator.TomogramSimulator property) (acryo.TomogramSimulator property) score (acryo.alignment.AlignmentResult attribute) set_backend() (in module acryo.backend) shape (acryo.backend.AnyArray property) shift (acryo.alignment.AlignmentResult attribute) shift() (in module acryo.pipe) simulate() (acryo.simulator.TomogramSimulator method) (acryo.TomogramSimulator method) simulate_2d() (acryo.simulator.TomogramSimulator method) (acryo.TomogramSimulator method) simulate_projection() (acryo.simulator.TomogramSimulator method) (acryo.TomogramSimulator method) simulate_tilt_series() (acryo.simulator.TomogramSimulator method) (acryo.TomogramSimulator method)

single_axis() (in module acryo.tilt) (in module acryo.tilt.core) SingleAxis (class in acryo.tilt) soft_otsu() (in module acryo.pipe) sort() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) spiral() (in module acryo.testing) spline_filter() (acryo.backend.Backend method) split_clusters() (acryo.classification.pca.PcaClassifier method) (acryo.classification.PcaClassifier method) sqrt() (acryo.backend.Backend method) stack() (acryo.backend.Backend method) subset() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) (acryo.simulator.TomogramSimulator method) (acryo.TomogramSimulator method) SubtomogramLoader (class in acryo) (class in acryo.loader) sum() (acryo.backend.Backend method)

T

tail() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) template (acryo.alignment.BaseAlignmentModel property) (acryo.testing.core.TomogramGenerator property) (acryo.testing.TomogramGenerator property) tensordot() (acryo.backend.Backend method) threshold_otsu() (in module acryo.pipe) tilt_range (acryo.tilt.SingleAxis property) TiltSeriesModel (class in acryo.tilt) to_csv() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) to_dataframe() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) to_file() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method)

to_parquet() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) TomogramGenerator (class in acryo.testing) (class in acryo.testing.core) TomogramSimulator (class in acryo) (class in acryo.simulator) TomographyInput (class in acryo.alignment) transform() (acryo.classification.pca.PcaClassifier method) (acryo.classification.PcaClassifier method) translate() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) translate_internal() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) translate_random() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method)

U

UnionAxes (class in acryo.tilt)

unravel_index() (acryo.backend.Backend method) using_backend() (in module acryo.backend)

W

with_features() (acryo.Molecules method) (acryo.molecules.core.Molecules method) (acryo.molecules.Molecules method) with_params() (acryo.alignment.BaseAlignmentModel class method) (acryo.alignment.RotationImplemented class method) (acryo.alignment.TomographyInput class method)

with_scale() (acryo.pipe.ImageConverter method) wrange() (in module acryo.testing.core)

X

x (acryo.Molecules property) (acryo.molecules.core.Molecules property) (acryo.molecules.Molecules property)

Y

y (acryo.Molecules property) (acryo.molecules.core.Molecules property) (acryo.molecules.Molecules property)

Z

z (acryo.Molecules property) (acryo.molecules.core.Molecules property) (acryo.molecules.Molecules property)

zeros() (acryo.backend.Backend method) ZNCCAlignment (class in acryo.alignment) ZNCCTemplateMatcher (class in acryo.pick)