Index

A

add_callbacks() (SwissKnife.model.Model method) add_result() (SwissKnife.utils.ResultsTracker method) apply_all_masks() (in module SwissKnife.utils)

apply_mask() (in module SwissKnife.visualization) apply_to_mask() (in module SwissKnife.utils) assign_ids() (SwissKnife.masksmoothing.MaskMatcher method)

B

BACKBONE (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute) balanced_acc() (in module SwissKnife.utils) BATCH_SIZE (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.InferenceConfigMouse attribute) (SwissKnife.segmentation.InferenceConfigPrimate attribute) (SwissKnife.segmentation.InferencIneichenConfig attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute)

bbox_mask() (in module SwissKnife.utils) bbox_match() (SwissKnife.masksmoothing.MaskMatcher method) bbox_to_polygon() (SwissKnife.masksmoothing.MaskMatcher method)

C

calculate_rmse() (in module SwissKnife.poseestimation) calculate_speed() (in module SwissKnife.utils) callbacks_learningRate_plateau() (in module SwissKnife.utils) callbacks_tf_logging() (in module SwissKnife.utils) callbacks_viz_poseestimation (class in SwissKnife.poseestimation) categorical_focal_loss() (in module SwissKnife.utils) categorize_data() (SwissKnife.dataloader.Dataloader method) change_dtype() (SwissKnife.dataloader.Dataloader method) check_directory() (in module SwissKnife.utils) check_folder() (in module SwissKnife.utils) classification_large() (in module SwissKnife.architectures)

classification_scratch() (in module SwissKnife.architectures) classification_small() (in module SwissKnife.architectures) clearMemory() (in module SwissKnife.utils) coords_to_masks() (in module SwissKnife.utils) create_dataset() (in module SwissKnife.dataloader) (SwissKnife.dataloader.Dataloader method) create_flattened_data() (SwissKnife.dataloader.Dataloader method) create_recurrent_data() (SwissKnife.dataloader.Dataloader method) create_recurrent_data_dlc() (SwissKnife.dataloader.Dataloader method) create_recurrent_labels() (SwissKnife.dataloader.Dataloader method) crop_pngs() (in module SwissKnife.utils) custom_binary_crossentropy() (in module SwissKnife.poseestimation)

D

DataGenerator (class in SwissKnife.poseestimation) Dataloader (class in SwissKnife.dataloader) Dataset (class in SwissKnife.dataprep) decimate_labels() (SwissKnife.dataloader.Dataloader method) decode_labels() (SwissKnife.dataloader.Dataloader method) detect_image() (SwissKnife.segmentation.SegModel method) detect_image_original() (SwissKnife.segmentation.SegModel method) detect_primate() (in module SwissKnife.utils) detect_video() (SwissKnife.segmentation.SegModel method) DETECTION_MAX_INSTANCES (SwissKnife.segmentation.PrimateConfig attribute) DETECTION_MIN_CONFIDENCE (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.InferenceConfigMouse attribute) (SwissKnife.segmentation.InferenceConfigPrimate attribute) (SwissKnife.segmentation.InferencIneichenConfig attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute)

dilate_mask() (in module SwissKnife.utils) displayBoxes() (in module SwissKnife.visualization) displayScatter() (in module SwissKnife.visualization) distance() (in module SwissKnife.utils) dlc_model() (in module SwissKnife.architectures) dlc_model_sturman() (in module SwissKnife.architectures) do_ablation() (in module SwissKnife.segmentation) downscale_frames() (SwissKnife.dataloader.Dataloader method)

E

encode_label() (SwissKnife.dataloader.Dataloader method) encode_labels() (SwissKnife.dataloader.Dataloader method) eval_model() (in module SwissKnife.utils) evaluate() (SwissKnife.segmentation.SegModel method) evaluate_network() (in module SwissKnife.segmentation)

evaluate_pose_estimation() (in module SwissKnife.poseestimation) expand_dims() (SwissKnife.dataloader.Dataloader method) export_training_details() (SwissKnife.model.Model method) extractCOM() (in module SwissKnife.utils) extractCOM_only() (in module SwissKnife.utils)

F

f1() (in module SwissKnife.utils) f1_loss() (in module SwissKnife.utils) file_available() (SwissKnife.utils.ResultsTracker method)

fix_layers() (in module SwissKnife.utils) fix_recognition_layers() (SwissKnife.model.Model method) full_inference() (in module SwissKnife.full_inference)

G

generate_individual_mouse_data() (in module SwissKnife.dataprep) generate_mouse_pose_data() (in module SwissKnife.dataprep) generate_primate_pose_data() (in module SwissKnife.dataprep) get_ax() (in module SwissKnife.utils) get_data() (SwissKnife.poseestimation.Metrics method) (SwissKnife.poseestimation.rmse_metric method) (SwissKnife.utils.Metrics method) get_individual_mouse_data() (in module SwissKnife.dataprep) get_input_shape() (SwissKnife.dataloader.Dataloader method) get_mouse_dlc_data() (in module SwissKnife.dataprep) get_mouse_pose_data() (in module SwissKnife.dataprep)

get_mouse_pose_dlc_comparison_data() (in module SwissKnife.dataprep) get_optimizer() (in module SwissKnife.utils) get_primate_identification_data() (in module SwissKnife.dataprep) get_primate_pose_data() (in module SwissKnife.dataprep) get_segmentation_data() (in module SwissKnife.dataprep) get_SIPEC_reproduction_data() (in module SwissKnife.dataprep) get_tensorbaord_callback() (in module SwissKnife.utils) GPU_COUNT (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute) GRADIENT_CLIP_NORM (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute)

H

heatmap_mask() (in module SwissKnife.utils) heatmap_to_scatter() (in module SwissKnife.utils) heatmaps_for_image() (in module SwissKnife.utils)

heatmaps_for_image_whole() (in module SwissKnife.utils) heatmaps_for_images() (in module SwissKnife.utils) heatmaps_to_locs() (in module SwissKnife.utils)

I

idtracker_ai() (in module SwissKnife.architectures) IMAGE_MAX_DIM (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.InferenceConfigPrimate attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute) IMAGE_MIN_DIM (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.InferenceConfigPrimate attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute) image_reference() (SwissKnife.dataprep.Dataset method) IMAGE_RESIZE_MODE (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.InferenceConfigPrimate attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute) IMAGE_SHAPE (SwissKnife.segmentation.InferenceConfigPrimate attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute)

IMAGES_PER_GPU (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.InferenceConfigMouse attribute) (SwissKnife.segmentation.InferenceConfigPrimate attribute) (SwissKnife.segmentation.InferencIneichenConfig attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute) IneichenConfig (class in SwissKnife.segmentation) InferenceConfigMouse (class in SwissKnife.segmentation) InferenceConfigPrimate (class in SwissKnife.segmentation) InferencIneichenConfig (class in SwissKnife.segmentation) init_augmentation() (SwissKnife.segmentation.SegModel method) init_training() (SwissKnife.segmentation.SegModel method) iou() (SwissKnife.masksmoothing.MaskMatcher method)

K

keypoints_in_mask() (in module SwissKnife.utils)

L

LEARNING_RATE (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute) load() (SwissKnife.dataprep.Dataset method) load_config() (in module SwissKnife.utils)

load_dict() (in module SwissKnife.utils) load_mask() (SwissKnife.dataprep.Dataset method) load_recognition_model() (SwissKnife.model.Model method) load_vgg_labels() (in module SwissKnife.utils) loadVideo() (in module SwissKnife.utils)

M

main() (in module SwissKnife.classification_comparison) (in module SwissKnife.dataprep) (in module SwissKnife.full_inference) (in module SwissKnife.job_runner) (in module SwissKnife.masksmoothing) (in module SwissKnife.poseestimation) (in module SwissKnife.segmentation) (in module SwissKnife.visualization) map() (SwissKnife.masksmoothing.MaskMatcher method) mask_to_original_image() (in module SwissKnife.utils) maskedImg() (in module SwissKnife.utils) MaskFilter (class in SwissKnife.segmentation) MaskMatcher (class in SwissKnife.masksmoothing) masks_to_coms() (in module SwissKnife.utils) masks_to_coords() (in module SwissKnife.utils) match_ids() (SwissKnife.masksmoothing.MaskMatcher method) match_masks() (SwissKnife.masksmoothing.MaskMatcher method) MAX_GT_INSTANCES (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute) Metrics (class in SwissKnife.poseestimation) (class in SwissKnife.utils) MINI_MASK_SHAPE (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute)

Model (class in SwissKnife.model) module SwissKnife SwissKnife.architectures SwissKnife.augmentations SwissKnife.classification_comparison SwissKnife.dataloader SwissKnife.dataprep SwissKnife.full_inference SwissKnife.job_runner SwissKnife.masksmoothing SwissKnife.model SwissKnife.poseestimation SwissKnife.segmentation SwissKnife.test SwissKnife.utils SwissKnife.visualization mold_image() (in module SwissKnife.segmentation) mold_video() (in module SwissKnife.segmentation) mouse_identification() (in module SwissKnife.augmentations) mouse_poseestimation() (in module SwissKnife.augmentations) MouseConfig (class in SwissKnife.segmentation)

N

NAME (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute)

normalize_data() (SwissKnife.dataloader.Dataloader method) NUM_CLASSES (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute)

O

on_epoch_end() (SwissKnife.poseestimation.callbacks_viz_poseestimation method) (SwissKnife.poseestimation.DataGenerator method) (SwissKnife.poseestimation.Metrics method) (SwissKnife.poseestimation.rmse_metric method) (SwissKnife.utils.Metrics method)

on_train_begin() (SwissKnife.poseestimation.callbacks_viz_poseestimation method) (SwissKnife.poseestimation.Metrics method) (SwissKnife.poseestimation.rmse_metric method) (SwissKnife.utils.Metrics method)

P

pathForFile() (in module SwissKnife.utils) plotHistory() (in module SwissKnife.utils) posenet() (in module SwissKnife.architectures) predict() (SwissKnife.model.Model method) (SwissKnife.segmentation.MaskFilter method) predict_sequential() (SwissKnife.model.Model method)

prepare_data() (SwissKnife.dataloader.Dataloader method) prepareData() (in module SwissKnife.dataprep) pretrained_recognition() (in module SwissKnife.architectures) primate_identification() (in module SwissKnife.augmentations) primate_poseestimation() (in module SwissKnife.augmentations) PrimateConfig (class in SwissKnife.segmentation)

R

read_DLC_data() (in module SwissKnife.poseestimation) read_dlc_labels_from_folder() (in module SwissKnife.poseestimation) recurrent_model_lstm() (in module SwissKnife.architectures) recurrent_model_old() (in module SwissKnife.architectures) recurrent_model_tcn() (in module SwissKnife.architectures) reduce_labels() (SwissKnife.dataloader.Dataloader method) remove_behavior() (SwissKnife.dataloader.Dataloader method) remove_classification_layers() (SwissKnife.model.Model method)

remove_layers() (in module SwissKnife.classification_comparison) rescale_img() (in module SwissKnife.utils) resize() (in module SwissKnife.utils) resize_image() (in module SwissKnife.utils) ResultsTracker (class in SwissKnife.utils) revert_mold() (in module SwissKnife.poseestimation) rmse_metric (class in SwissKnife.poseestimation) run_ai_cumulative_gradient() (in module SwissKnife.utils) run_experiment() (in module SwissKnife.classification_comparison)

S

save_dict() (in module SwissKnife.utils) save_model() (SwissKnife.model.Model method) saveModel() (in module SwissKnife.utils) scheduler() (SwissKnife.model.Model method) segment_images_and_masks() (in module SwissKnife.poseestimation) SegModel (class in SwissKnife.segmentation) set_augmentation() (SwissKnife.model.Model method) set_class_weight() (SwissKnife.model.Model method) set_inference() (SwissKnife.segmentation.SegModel method) set_lr_scheduler() (SwissKnife.model.Model method) set_optimizer() (SwissKnife.model.Model method) set_random_seed() (in module SwissKnife.utils) set_recognition_model() (SwissKnife.model.Model method) set_sequential_model() (SwissKnife.model.Model method) setGPU() (in module SwissKnife.utils) setGPU_growth() (in module SwissKnife.utils) setModel() (SwissKnife.poseestimation.callbacks_viz_poseestimation method) (SwissKnife.poseestimation.Metrics method) (SwissKnife.poseestimation.rmse_metric method) (SwissKnife.utils.Metrics method) SkipConNet() (in module SwissKnife.architectures) startend() (in module SwissKnife.utils) STEPS_PER_EPOCH (SwissKnife.segmentation.IneichenConfig attribute) (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute) SwissKnife module

SwissKnife.architectures module SwissKnife.augmentations module SwissKnife.classification_comparison module SwissKnife.dataloader module SwissKnife.dataprep module SwissKnife.full_inference module SwissKnife.job_runner module SwissKnife.masksmoothing module SwissKnife.model module SwissKnife.poseestimation module SwissKnife.segmentation module SwissKnife.test module SwissKnife.utils module SwissKnife.visualization module

T

train() (SwissKnife.segmentation.MaskFilter method) (SwissKnife.segmentation.SegModel method) train_model() (in module SwissKnife.utils) train_on_data() (in module SwissKnife.poseestimation) (in module SwissKnife.segmentation) train_on_data_once() (in module SwissKnife.segmentation)

train_on_data_path() (in module SwissKnife.segmentation) train_recognition_network() (SwissKnife.model.Model method) TRAIN_ROIS_PER_IMAGE (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute) train_sequential_network() (SwissKnife.model.Model method) treshold_maps() (in module SwissKnife.poseestimation)

U

undersample_data() (SwissKnife.dataloader.Dataloader method) update_params() (SwissKnife.model.Model method)

USE_MINI_MASK (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute)

V

vis_locs() (in module SwissKnife.poseestimation) vis_maps() (in module SwissKnife.poseestimation)

visualize_full_inference() (in module SwissKnife.visualization) visualize_labels_on_video() (in module SwissKnife.visualization) visualize_labels_on_video_cv() (in module SwissKnife.visualization)

W

WEIGHT_DECAY (SwissKnife.segmentation.MouseConfig attribute) (SwissKnife.segmentation.PrimateConfig attribute)

write_results() (SwissKnife.utils.ResultsTracker method)