Index

Symbols

--camera-type moseq2-pca-train-pca command line option --chunk-size moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --cluster-type moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --config-file moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --cores moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --dask-cache-path moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --dask-port moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --detrend-window moseq2-pca-apply-pca command line option --dims moseq2-pca-compute-changepoints command line option --fill-gaps moseq2-pca-apply-pca command line option --fps moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option --from-end moseq2-pca-clip-scores command line option --gaussfilter-space moseq2-pca-train-pca command line option --gaussfilter-time moseq2-pca-train-pca command line option --h5-mask-path moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --h5-path moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --input-dir moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --klags moseq2-pca-compute-changepoints command line option --local-processes moseq2-pca-train-pca command line option --mask-height-threshold moseq2-pca-train-pca command line option --mask-threshold moseq2-pca-train-pca command line option --max-height moseq2-pca-train-pca command line option --medfilter-space moseq2-pca-train-pca command line option --medfilter-time moseq2-pca-train-pca command line option --memory moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --min-height moseq2-pca-train-pca command line option --missing-data moseq2-pca-train-pca command line option --missing-data-iters moseq2-pca-train-pca command line option --neighbors moseq2-pca-compute-changepoints command line option --nworkers moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --output-dir moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --output-file moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --overwrite-pca-apply moseq2-pca-apply-pca command line option

--overwrite-pca-train moseq2-pca-train-pca command line option --pca-file moseq2-pca-apply-pca command line option --pca-file-components moseq2-pca-compute-changepoints command line option --pca-file-scores moseq2-pca-compute-changepoints command line option --pca-path moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option --processes moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --queue moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --rank moseq2-pca-train-pca command line option --recon-pcs moseq2-pca-train-pca command line option --sigma moseq2-pca-compute-changepoints command line option --tailfilter-shape moseq2-pca-train-pca command line option --tailfilter-size moseq2-pca-train-pca command line option --threshold moseq2-pca-compute-changepoints command line option --timeout moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option --train-on-subset moseq2-pca-train-pca command line option --use-fft moseq2-pca-train-pca command line option --verbose moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option --version moseq2-pca command line option --wall-time moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option -c moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option -d moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option, [1] moseq2-pca-train-pca command line option -i moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option -k moseq2-pca-compute-changepoints command line option -m moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option -n moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option -o moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option -p moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option -q moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option -s moseq2-pca-compute-changepoints command line option -v moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option -w moseq2-pca-apply-pca command line option moseq2-pca-compute-changepoints command line option moseq2-pca-train-pca command line option

A

apply_pca_command() (in module moseq2_pca.gui) apply_pca_dask() (in module moseq2_pca.pca.util)

apply_pca_local() (in module moseq2_pca.pca.util) apply_pca_wrapper() (in module moseq2_pca.helpers.wrappers)

C

changepoint_dist() (in module moseq2_pca.viz) check_timestamps() (in module moseq2_pca.util) clean_frames() (in module moseq2_pca.util) CLIP_SAMPLES moseq2-pca-clip-scores command line option clip_scores_wrapper() (in module moseq2_pca.helpers.wrappers) close_dask() (in module moseq2_pca.util)

combine_new_config() (in module moseq2_pca.util) command_with_config() (in module moseq2_pca.util) compute_changepoints_command() (in module moseq2_pca.gui) compute_changepoints_wrapper() (in module moseq2_pca.helpers.wrappers) compute_explained_variance() (in module moseq2_pca.pca.util) compute_svd() (in module moseq2_pca.pca.util) copy_metadatas_to_scores() (in module moseq2_pca.pca.util)

D

display_components() (in module moseq2_pca.viz)

G

gauss_smooth() (in module moseq2_pca.util) gaussian_kernel1d() (in module moseq2_pca.util) get_changepoints() (in module moseq2_pca.util) get_changepoints_dask() (in module moseq2_pca.pca.util) get_env_cpu_and_mem() (in module moseq2_pca.util)

get_metadata_path() (in module moseq2_pca.util) get_pca_paths() (in module moseq2_pca.helpers.data) get_pca_yaml_data() (in module moseq2_pca.helpers.data) get_rps() (in module moseq2_pca.util) get_timestamp_path() (in module moseq2_pca.util) get_timestamps() (in module moseq2_pca.pca.util)

H

h5_to_dict() (in module moseq2_pca.util)

I

initialize_dask() (in module moseq2_pca.util)

insert_nans() (in module moseq2_pca.util)

L

load_and_check_data() (in module moseq2_pca.helpers.wrappers)

load_pcs_for_cp() (in module moseq2_pca.helpers.data)

M

mask_data() (in module moseq2_pca.pca.util) module moseq2_pca.gui moseq2_pca.helpers.data moseq2_pca.helpers.wrappers moseq2_pca.pca.util moseq2_pca.util moseq2_pca.viz moseq2-pca command line option --version moseq2-pca-apply-pca command line option --chunk-size --cluster-type --config-file --cores --dask-cache-path --dask-port --detrend-window --fill-gaps --fps --h5-mask-path --h5-path --input-dir --memory --nworkers --output-dir --output-file --overwrite-pca-apply --pca-file --pca-path --processes --queue --timeout --verbose --wall-time -c -d -i -m -n -o -p -q -v -w moseq2-pca-clip-scores command line option --from-end CLIP_SAMPLES PCA_FILE moseq2-pca-compute-changepoints command line option --chunk-size --cluster-type --config-file --cores --dask-cache-path --dask-port --dims --fps --h5-mask-path --h5-path --input-dir --klags --memory --neighbors --nworkers --output-dir --output-file --pca-file-components --pca-file-scores --pca-path --processes --queue --sigma --threshold --timeout --verbose --wall-time -c -d, [1] -i -k -m -n -o -p -q -s -v -w

moseq2-pca-train-pca command line option --camera-type --chunk-size --cluster-type --config-file --cores --dask-cache-path --dask-port --gaussfilter-space --gaussfilter-time --h5-mask-path --h5-path --input-dir --local-processes --mask-height-threshold --mask-threshold --max-height --medfilter-space --medfilter-time --memory --min-height --missing-data --missing-data-iters --nworkers --output-dir --output-file --overwrite-pca-train --processes --queue --rank --recon-pcs --tailfilter-shape --tailfilter-size --timeout --train-on-subset --use-fft --wall-time -c -d -i -m -n -o -p -q -w moseq2_pca.gui module moseq2_pca.helpers.data module moseq2_pca.helpers.wrappers module moseq2_pca.pca.util module moseq2_pca.util module moseq2_pca.viz module

P

PCA_FILE moseq2-pca-clip-scores command line option

plot_pca_results() (in module moseq2_pca.viz)

R

read_yaml() (in module moseq2_pca.util)

recursive_find_h5s() (in module moseq2_pca.util)

S

scree_plot() (in module moseq2_pca.viz)

select_strel() (in module moseq2_pca.util) set_dask_config() (in module moseq2_pca.util)

T

train_pca_command() (in module moseq2_pca.gui)

train_pca_dask() (in module moseq2_pca.pca.util) train_pca_wrapper() (in module moseq2_pca.helpers.wrappers)