Index

Symbols

--angle-hampel-sig moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --angle-hampel-span moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --bg-roi-depth-range moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-roi-dilate moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-roi-erode moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-roi-fill-holes moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-roi-gradient-filter moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-roi-gradient-kernel moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-roi-gradient-threshold moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-roi-index moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-roi-shape moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-roi-weights moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-sort-roi-by-position moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --bg-sort-roi-by-position-max-rois moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --cable-filter-iters moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --cable-filter-shape moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --cable-filter-size moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --camera-type moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option moseq2-extract-generate-config command line option --centroid-hampel-sig moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --centroid-hampel-span moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --chunk-overlap moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --chunk-size moseq2-extract-batch-extract command line option moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option --cluster-type moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --compress moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --compress-chunk-size moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --compress-threads moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --compute-raw-scalars moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --config-file moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --copy-slice moseq2-extract-copy-slice command line option --crop-size moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --delete moseq2-extract-batch-extract command line option moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option --detected-true-depth moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --dilate-iterations moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --erode-iterations moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --extensions moseq2-extract-batch-extract command line option --extract-out-script moseq2-extract-batch-extract command line option --flip-classifier moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --flip-classifier-smoothing moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --format moseq2-extract-aggregate-results command line option --fps moseq2-extract-batch-extract command line option moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option --frame-dtype moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --frame-trim moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --get-cmd moseq2-extract-batch-extract command line option --graduate-walls moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --input-dir moseq2-extract-agg-to-index command line option moseq2-extract-aggregate-results command line option moseq2-extract-generate-index command line option --manual-set-depth-range moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --mapping moseq2-extract-batch-extract command line option moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option

--max-height moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --memory moseq2-extract-batch-extract command line option --min-height moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --model-smoothing-clips moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --mouse-threshold moseq2-extract-aggregate-results command line option --movie-dtype moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --ncpus moseq2-extract-batch-extract command line option --noise-tolerance moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --num-frames moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --output-dir moseq2-extract-aggregate-results command line option moseq2-extract-batch-extract command line option moseq2-extract-download-flip-file command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --output-file moseq2-extract-batch-extract command line option moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option moseq2-extract-generate-config command line option moseq2-extract-generate-index command line option --partition moseq2-extract-batch-extract command line option --pixel-format moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --prefix moseq2-extract-batch-extract command line option --progress-bar moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --recompute-bg moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --run-cmd moseq2-extract-batch-extract command line option --skip-checks moseq2-extract-batch-extract command line option --skip-completed moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --spatial-filter-size moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --tail-filter-iters moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --tail-filter-shape moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --tail-filter-size moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --temporal-filter-size moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --threads moseq2-extract-batch-extract command line option moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option --tracking-model-init moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --tracking-model-ll-clip moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --tracking-model-ll-threshold moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --tracking-model-mask-threshold moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --tracking-model-segment moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --use-cc moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --use-plane-bground moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option --use-tracking-model moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --version moseq2-extract command line option --wall-time moseq2-extract-batch-extract command line option --widen-radius moseq2-extract-batch-extract command line option moseq2-extract-extract command line option --write-movie moseq2-extract-batch-extract command line option moseq2-extract-extract command line option -b moseq2-extract-batch-extract command line option moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option -c moseq2-extract-batch-extract command line option, [1] moseq2-extract-copy-slice command line option moseq2-extract-extract command line option -f moseq2-extract-aggregate-results command line option -i moseq2-extract-agg-to-index command line option moseq2-extract-aggregate-results command line option moseq2-extract-generate-index command line option -m moseq2-extract-batch-extract command line option moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option -n moseq2-extract-batch-extract command line option moseq2-extract-extract command line option -o moseq2-extract-aggregate-results command line option moseq2-extract-batch-extract command line option moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option moseq2-extract-generate-config command line option moseq2-extract-generate-index command line option -p moseq2-extract-batch-extract command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option -s moseq2-extract-batch-extract command line option moseq2-extract-extract command line option -t moseq2-extract-batch-extract command line option, [1] moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option, [1]

A

aggregate_extract_results_wrapper() (in module moseq2_extract.helpers.wrappers)

apply_roi() (in module moseq2_extract.extract.proc)

B

build_index_dict() (in module moseq2_extract.helpers.data)

build_manifest() (in module moseq2_extract.helpers.data) build_path() (in module moseq2_extract.util)

C

camel_to_snake() (in module moseq2_extract.util) check_completion_status() (in module moseq2_extract.helpers.data) check_filter_sizes() (in module moseq2_extract.util) clean_dict() (in module moseq2_extract.util) clean_file_str() (in module moseq2_extract.util) clean_frames() (in module moseq2_extract.extract.proc) click_param_annot() (in module moseq2_extract.util) command_with_config() (in module moseq2_extract.util) compute_scalars() (in module moseq2_extract.extract.proc)

CONFIG_FILE moseq2-extract-download-flip-file command line option convert_pxs_to_mm() (in module moseq2_extract.util) convert_raw_to_avi_function() (in module moseq2_extract.util) convert_raw_to_avi_wrapper() (in module moseq2_extract.helpers.wrappers) copy_h5_metadata_to_yaml_wrapper() (in module moseq2_extract.helpers.wrappers) copy_manifest_results() (in module moseq2_extract.helpers.data) copy_slice_wrapper() (in module moseq2_extract.helpers.wrappers) create_extract_h5() (in module moseq2_extract.helpers.data) crop_and_rotate_frames() (in module moseq2_extract.extract.proc)

D

detect_and_set_camera_parameters() (in module moseq2_extract.util) detect_avi_file() (in module moseq2_extract.util)

dict_to_h5() (in module moseq2_extract.util) download_flip_command() (in module moseq2_extract.gui)

E

em_get_ll() (in module moseq2_extract.extract.track) em_init() (in module moseq2_extract.extract.track) em_iter() (in module moseq2_extract.extract.track)

em_tracking() (in module moseq2_extract.extract.track) escape_path() (in module moseq2_extract.util) extract_chunk() (in module moseq2_extract.extract.extract) extract_wrapper() (in module moseq2_extract.helpers.wrappers)

F

feature_hampel_filter() (in module moseq2_extract.extract.proc)

filter_warnings() (in module moseq2_extract.util)

G

gen_batch_sequence() (in module moseq2_extract.util) generate_index_command() (in module moseq2_extract.gui) generate_index_from_agg_res_wrapper() (in module moseq2_extract.helpers.wrappers) generate_missing_metadata() (in module moseq2_extract.util) get_bbox() (in module moseq2_extract.extract.proc) get_bground_im_file() (in module moseq2_extract.extract.proc) get_bucket_center() (in module moseq2_extract.util) get_flips() (in module moseq2_extract.extract.proc) get_frame_features() (in module moseq2_extract.extract.proc) get_frame_range_indices() (in module moseq2_extract.util)

get_largest_cc() (in module moseq2_extract.extract.proc) get_movie_info() (in module moseq2_extract.io.video) get_raw_info() (in module moseq2_extract.io.video) get_roi() (in module moseq2_extract.extract.proc) get_roi_wrapper() (in module moseq2_extract.helpers.wrappers) get_selected_sessions() (in module moseq2_extract.gui) get_stream_names() (in module moseq2_extract.io.video) get_strels() (in module moseq2_extract.util) get_video_info() (in module moseq2_extract.io.video) graduate_dilated_wall_area() (in module moseq2_extract.util)

H

h5_to_dict() (in module moseq2_extract.util)

handle_extract_metadata() (in module moseq2_extract.helpers.data)

I

im_moment_features() (in module moseq2_extract.extract.proc) INPUT_FILE moseq2-extract-convert-raw-to-avi command line option moseq2-extract-copy-slice command line option moseq2-extract-extract command line option moseq2-extract-find-roi command line option

INPUT_FOLDER moseq2-extract-batch-extract command line option

L

load_extraction_meta_from_h5s() (in module moseq2_extract.helpers.data) load_found_session_paths() (in module moseq2_extract.util) load_metadata() (in module moseq2_extract.util)

load_movie_data() (in module moseq2_extract.io.video) load_textdata() (in module moseq2_extract.util) load_timestamps() (in module moseq2_extract.util) load_timestamps_from_movie() (in module moseq2_extract.io.video)

M

make_gradient() (in module moseq2_extract.util) make_output_movie() (in module moseq2_extract.helpers.extract) model_smoother() (in module moseq2_extract.extract.proc) module moseq2_extract.extract.extract moseq2_extract.extract.proc moseq2_extract.extract.roi moseq2_extract.extract.track moseq2_extract.gui moseq2_extract.helpers.data moseq2_extract.helpers.extract moseq2_extract.helpers.wrappers moseq2_extract.io.image moseq2_extract.io.video moseq2_extract.util moseq2-extract command line option --version moseq2-extract-agg-to-index command line option --input-dir -i moseq2-extract-aggregate-results command line option --format --input-dir --mouse-threshold --output-dir -f -i -o moseq2-extract-batch-extract command line option --angle-hampel-sig --angle-hampel-span --bg-roi-depth-range --bg-roi-dilate --bg-roi-erode --bg-roi-fill-holes --bg-roi-gradient-filter --bg-roi-gradient-kernel --bg-roi-gradient-threshold --bg-roi-index --bg-roi-shape --bg-roi-weights --bg-sort-roi-by-position --bg-sort-roi-by-position-max-rois --cable-filter-iters --cable-filter-shape --cable-filter-size --camera-type --centroid-hampel-sig --centroid-hampel-span --chunk-overlap --chunk-size --cluster-type --compress --compress-chunk-size --compress-threads --compute-raw-scalars --config-file --crop-size --delete --detected-true-depth --dilate-iterations --erode-iterations --extensions --extract-out-script --flip-classifier --flip-classifier-smoothing --fps --frame-dtype --frame-trim --get-cmd --graduate-walls --manual-set-depth-range --mapping --max-height --memory --min-height --model-smoothing-clips --movie-dtype --ncpus --noise-tolerance --num-frames --output-dir --output-file --partition --pixel-format --prefix --progress-bar --recompute-bg --run-cmd --skip-checks --skip-completed --spatial-filter-size --tail-filter-iters --tail-filter-shape --tail-filter-size --temporal-filter-size --threads --tracking-model-init --tracking-model-ll-clip --tracking-model-ll-threshold --tracking-model-mask-threshold --tracking-model-segment --use-cc --use-plane-bground --use-tracking-model --wall-time --widen-radius --write-movie -b -c, [1] -m -n -o -p -s -t, [1] INPUT_FOLDER moseq2-extract-convert-raw-to-avi command line option --chunk-size --delete --fps --mapping --output-file --threads -b -m -o -t INPUT_FILE moseq2-extract-copy-slice command line option --chunk-size --copy-slice --delete --fps --mapping --output-file --threads -b -c -m -o -t INPUT_FILE

moseq2-extract-download-flip-file command line option --output-dir CONFIG_FILE moseq2-extract-extract command line option --angle-hampel-sig --angle-hampel-span --bg-roi-depth-range --bg-roi-dilate --bg-roi-erode --bg-roi-fill-holes --bg-roi-gradient-filter --bg-roi-gradient-kernel --bg-roi-gradient-threshold --bg-roi-index --bg-roi-shape --bg-roi-weights --bg-sort-roi-by-position --bg-sort-roi-by-position-max-rois --cable-filter-iters --cable-filter-shape --cable-filter-size --camera-type --centroid-hampel-sig --centroid-hampel-span --chunk-overlap --chunk-size --cluster-type --compress --compress-chunk-size --compress-threads --compute-raw-scalars --config-file --crop-size --delete --detected-true-depth --dilate-iterations --erode-iterations --flip-classifier --flip-classifier-smoothing --fps --frame-dtype --frame-trim --graduate-walls --manual-set-depth-range --mapping --max-height --min-height --model-smoothing-clips --movie-dtype --noise-tolerance --num-frames --output-dir --output-file --pixel-format --progress-bar --recompute-bg --skip-completed --spatial-filter-size --tail-filter-iters --tail-filter-shape --tail-filter-size --temporal-filter-size --threads --tracking-model-init --tracking-model-ll-clip --tracking-model-ll-threshold --tracking-model-mask-threshold --tracking-model-segment --use-cc --use-plane-bground --use-tracking-model --widen-radius --write-movie -b -c -m -n -o -p -s -t, [1] INPUT_FILE moseq2-extract-find-roi command line option --bg-roi-depth-range --bg-roi-dilate --bg-roi-erode --bg-roi-fill-holes --bg-roi-gradient-filter --bg-roi-gradient-kernel --bg-roi-gradient-threshold --bg-roi-index --bg-roi-shape --bg-roi-weights --bg-sort-roi-by-position --bg-sort-roi-by-position-max-rois --camera-type --config-file --dilate-iterations --erode-iterations --manual-set-depth-range --noise-tolerance --output-dir --progress-bar --recompute-bg --use-plane-bground -p INPUT_FILE moseq2-extract-generate-config command line option --camera-type --output-file -o moseq2-extract-generate-index command line option --input-dir --output-file -i -o moseq2_extract.extract.extract module moseq2_extract.extract.proc module moseq2_extract.extract.roi module moseq2_extract.extract.track module moseq2_extract.gui module moseq2_extract.helpers.data module moseq2_extract.helpers.extract module moseq2_extract.helpers.wrappers module moseq2_extract.io.image module moseq2_extract.io.video module moseq2_extract.util module mouse_threshold_filter() (in module moseq2_extract.util)

P

plane_fit3() (in module moseq2_extract.extract.roi)

plane_ransac() (in module moseq2_extract.extract.roi) process_extract_batches() (in module moseq2_extract.helpers.extract)

R

read_frames() (in module moseq2_extract.io.video) read_frames_raw() (in module moseq2_extract.io.video) read_image() (in module moseq2_extract.io.image) read_mkv() (in module moseq2_extract.io.video) read_tiff_files() (in module moseq2_extract.io.image)

read_yaml() (in module moseq2_extract.util) recursive_find_h5s() (in module moseq2_extract.util) recursive_find_unextracted_dirs() (in module moseq2_extract.util) run_local_extract() (in module moseq2_extract.helpers.extract) run_slurm_extract() (in module moseq2_extract.helpers.extract)

S

scalar_attributes() (in module moseq2_extract.util) select_strel() (in module moseq2_extract.util)

set_bground_to_plane_fit() (in module moseq2_extract.util) set_tracking_model_parameters() (in module moseq2_extract.helpers.extract) strided_app() (in module moseq2_extract.util)

T

threshold_chunk() (in module moseq2_extract.extract.proc)

time_str_for_filename() (in module moseq2_extract.util)

W

write_extracted_chunk_to_h5() (in module moseq2_extract.helpers.extract) write_frames() (in module moseq2_extract.io.video)

write_frames_preview() (in module moseq2_extract.io.video) write_image() (in module moseq2_extract.io.image)