Index

Symbols

--axes <AXES> qaa-cluster command line option, [1] --azim <AZIMUTH> qaa-cluster command line option --bias qaa-pca command line option --centroid <FILE> qaa-cluster command line option --cluster qaa-cluster command line option --dp <n_points> qaa-cluster command line option --dpi <DPI> qaa-cluster command line option --dpi <dpi> qaa-pca command line option --dt <OFFSET> qaa-align command line option qaa-pca command line option qaa-qaa command line option --elev <ELEVATION> qaa-cluster command line option --fastica qaa-qaa command line option --gmm qaa-cluster command line option --ica qaa-cluster command line option, [1] --infile <FILE> qaa-cluster command line option, [1] --it <image_type> qaa-pca command line option --iter <MAXITER> qaa-cluster command line option qaa-qaa command line option --jade qaa-qaa command line option --kmeans qaa-cluster command line option --label <FILE> qaa-cluster command line option --logfile <LOG> qaa-align command line option qaa-cluster command line option, [1] qaa-pca command line option qaa-qaa command line option --mask <mask> qaa-align command line option qaa-pca command line option qaa-qaa command line option --nclusters <n_clusters> qaa-cluster command line option --nmodes <NMODES> qaa-pca command line option qaa-qaa command line option --no-bias qaa-pca command line option --outdir <DIR> qaa-cluster command line option qaa-pca command line option qaa-qaa command line option --outfile <FILE> qaa-align command line option qaa-cluster command line option --pca qaa-cluster command line option, [1] --ref <FILE> qaa-align command line option

--save qaa-cluster command line option --tol <TOL> qaa-cluster command line option qaa-qaa command line option --tol <tol> qaa-align command line option --top <FILE> qaa-align command line option qaa-cluster command line option qaa-pca command line option qaa-qaa command line option --traj <FILE> qaa-align command line option qaa-cluster command line option qaa-pca command line option qaa-qaa command line option --verbose qaa-align command line option qaa-cluster command line option, [1] qaa-pca command line option qaa-qaa command line option --version qaa command line option --whiten qaa-pca command line option qaa-qaa command line option -c qaa-cluster command line option -f qaa-align command line option qaa-cluster command line option qaa-pca command line option qaa-qaa command line option -i qaa-cluster command line option, [1] -l qaa-align command line option qaa-cluster command line option, [1] qaa-pca command line option qaa-qaa command line option -m qaa-align command line option qaa-pca command line option qaa-qaa command line option -n qaa-cluster command line option qaa-pca command line option qaa-qaa command line option -o qaa-align command line option qaa-cluster command line option, [1] qaa-pca command line option qaa-qaa command line option -r qaa-align command line option -s qaa-align command line option qaa-cluster command line option qaa-pca command line option qaa-qaa command line option -v qaa-align command line option qaa-cluster command line option, [1] qaa-pca command line option qaa-qaa command line option -w qaa-pca command line option qaa-qaa command line option

A

align_trajectory() (in module qaa.libs.align)

D

draw() (qaa.libs.figure.Figure method)

F

Figure (class in qaa.libs.figure) figure (qaa.libs.figure.Figure attribute) find_closest_point() (in module qaa.commands.cmd_cluster)

fit() (qaa.decomposition.jade.JadeICA method) (qaa.libs.kabsch.Kabsch method) fit_transform() (qaa.decomposition.jade.JadeICA method)

G

get_average_structure() (in module qaa.libs.utils)

get_positions() (in module qaa.libs.utils)

I

inverse_transform() (qaa.decomposition.jade.JadeICA method)

J

JadeICA (class in qaa.decomposition.jade)

K

Kabsch (class in qaa.libs.kabsch)

M

module qaa.__main__ qaa.cli qaa.commands.cmd_align qaa.commands.cmd_cluster qaa.commands.cmd_pca qaa.commands.cmd_qaa qaa.decomposition.jade qaa.libs.align qaa.libs.figure qaa.libs.kabsch qaa.libs.utils

Q

qaa command line option --version qaa-align command line option --dt <OFFSET> --logfile <LOG> --mask <mask> --outfile <FILE> --ref <FILE> --tol <tol> --top <FILE> --traj <FILE> --verbose -f -l -m -o -r -s -v qaa-cluster command line option --axes <AXES>, [1] --azim <AZIMUTH> --centroid <FILE> --cluster --dp <n_points> --dpi <DPI> --elev <ELEVATION> --gmm --ica, [1] --infile <FILE>, [1] --iter <MAXITER> --kmeans --label <FILE> --logfile <LOG>, [1] --nclusters <n_clusters> --outdir <DIR> --outfile <FILE> --pca, [1] --save --tol <TOL> --top <FILE> --traj <FILE> --verbose, [1] -c -f -i, [1] -l, [1] -n -o, [1] -s -v, [1] qaa-pca command line option --bias --dpi <dpi> --dt <OFFSET> --it <image_type> --logfile <LOG> --mask <mask> --nmodes <NMODES> --no-bias --outdir <DIR> --top <FILE> --traj <FILE> --verbose --whiten -f -l -m -n -o -s -v -w

qaa-qaa command line option --dt <OFFSET> --fastica --iter <MAXITER> --jade --logfile <LOG> --mask <mask> --nmodes <NMODES> --outdir <DIR> --tol <TOL> --top <FILE> --traj <FILE> --verbose --whiten -f -l -m -n -o -s -v -w qaa.__main__ module qaa.cli module qaa.commands.cmd_align module qaa.commands.cmd_cluster module qaa.commands.cmd_pca module qaa.commands.cmd_qaa module qaa.decomposition.jade module qaa.libs.align module qaa.libs.figure module qaa.libs.kabsch module qaa.libs.utils module

R

reshape_positions() (in module qaa.libs.utils)

rmse() (in module qaa.libs.utils)

S

save() (qaa.libs.figure.Figure method)

T

transform() (qaa.decomposition.jade.JadeICA method) (qaa.libs.kabsch.Kabsch method)