TRex
Contents:
Installation
Usage basics
Updating the App
Usage examples
Using the graphical user interface
Visual Identification
Batch processing support
Examples
File formats
TRex parameters
TGrabs parameters
Frequently asked questions and solutions to weird problems
TRex
»
Index
Index
A
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B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
A
adaptive_threshold_scale()
built-in function
analysis_paused()
built-in function
analysis_range()
built-in function
app_check_for_updates()
built-in function
app_last_update_check()
built-in function
app_last_update_version()
built-in function
app_name()
built-in function
approximate_length_minutes()
built-in function
auto_apply()
built-in function
auto_categorize()
built-in function
auto_minmax_size()
built-in function
auto_no_memory_stats()
built-in function
auto_no_results()
built-in function
auto_no_tracking_data()
built-in function
auto_number_individuals()
built-in function
auto_quit()
built-in function
auto_tags()
built-in function
auto_tags_on_startup()
built-in function
auto_train()
built-in function
auto_train_dont_apply()
built-in function
auto_train_on_startup()
built-in function
average_samples()
built-in function
averaging_method()
built-in function
B
blob_size_range()
built-in function
blob_size_ranges()
built-in function
blob_split_algorithm()
built-in function
blob_split_global_shrink_limit()
built-in function
blob_split_max_shrink()
built-in function
blobs_per_thread()
built-in function
build()
built-in function
build_architecture()
built-in function
build_cxx_options()
built-in function
build_is_debug()
built-in function
build_type()
built-in function
built-in function
adaptive_threshold_scale()
analysis_paused()
analysis_range()
app_check_for_updates()
app_last_update_check()
app_last_update_version()
app_name()
approximate_length_minutes()
auto_apply()
auto_categorize()
auto_minmax_size()
auto_no_memory_stats()
auto_no_results()
auto_no_tracking_data()
auto_number_individuals()
auto_quit()
auto_tags()
auto_tags_on_startup()
auto_train()
auto_train_dont_apply()
auto_train_on_startup()
average_samples()
averaging_method()
blob_size_range()
blob_size_ranges()
blob_split_algorithm()
blob_split_global_shrink_limit()
blob_split_max_shrink()
blobs_per_thread()
build()
build_architecture()
build_cxx_options()
build_is_debug()
build_type()
calculate_posture()
cam_circle_mask()
cam_framerate()
cam_limit_exposure()
cam_matrix()
cam_resolution()
cam_scale()
cam_undistort()
cam_undistort_vector()
categories_min_sample_images()
categories_ordered()
closing_size()
cm_per_pixel()
cmd_line()
color_channel()
correct_illegal_lines()
correct_luminance()
crop_offsets()
crop_window()
debug()
debug_recognition_output_all_methods()
dilation_size()
enable_absolute_difference()
enable_closed_loop()
enable_difference()
enable_live_tracking()
equalize_histogram()
error_terminate()
event_min_peak_offset()
exec()
ffmpeg_crf()
ffmpeg_path()
filename()
fishdata_dir()
frame_rate()
gpu_accepted_uniqueness()
gpu_accumulation_enable_final_step()
gpu_accumulation_max_segments()
gpu_enable_accumulation()
gpu_learning_rate()
gpu_max_cache()
gpu_max_epochs()
gpu_max_sample_gb()
gpu_min_elements()
gpu_min_iterations()
gpu_verbosity()
grabber_force_settings()
grid_points()
grid_points_scaling()
gui_auto_scale()
gui_auto_scale_focus_one()
gui_background_color()
gui_connectivity_matrix()
gui_connectivity_matrix_file()
gui_draw_only_filtered_out()
gui_equalize_blob_histograms()
gui_faded_brightness()
gui_fish_color()
gui_focus_group()
gui_foi_name()
gui_foi_types()
gui_frame()
gui_happy_mode()
gui_highlight_categories()
gui_interface_scale()
gui_max_path_time()
gui_mode()
gui_outline_thickness()
gui_playback_speed()
gui_recording_format()
gui_run()
gui_show_blobs()
gui_show_boundary_crossings()
gui_show_cliques()
gui_show_dataset()
gui_show_detailed_probabilities()
gui_show_export_options()
gui_show_fish()
gui_show_graph()
gui_show_heatmap()
gui_show_histograms()
gui_show_inactive_individuals()
gui_show_match_modes()
gui_show_memory_stats()
gui_show_midline()
gui_show_midline_histogram()
gui_show_number_individuals()
gui_show_only_unassigned()
gui_show_outline()
gui_show_paths()
gui_show_pixel_grid()
gui_show_posture()
gui_show_probabilities()
gui_show_recognition_bounds()
gui_show_recognition_summary()
gui_show_selections()
gui_show_shadows()
gui_show_texts()
gui_show_uniqueness()
gui_show_visualfield()
gui_show_visualfield_ts()
gui_single_identity_color()
gui_timeline_alpha()
gui_transparent_background()
gui_zoom_limit()
heatmap_dynamic()
heatmap_frames()
heatmap_ids()
heatmap_normalization()
heatmap_resolution()
heatmap_smooth()
heatmap_source()
heatmap_value_range()
history_matching_log()
httpd_accepted_ip()
httpd_port()
huge_timestamp_ends_segment()
huge_timestamp_seconds()
image_adjust()
image_brightness_increase()
image_contrast_increase()
image_invert()
image_square_brightness()
individual_names()
individual_prefix()
individuals_per_thread()
limit()
log_file()
manual_identities()
manual_matches()
manual_splits()
manually_approved()
mask_path()
match_mode()
matching_probability_threshold()
meta_age_days()
meta_build()
meta_cmd()
meta_conditions()
meta_conversion_time()
meta_mass_mg()
meta_misc()
meta_real_width()
meta_source_path()
meta_species()
meta_write_these()
midline_invert()
midline_resolution()
midline_samples()
midline_start_with_head()
midline_stiff_percentage()
midline_walk_offset()
nowindow()
,
[1]
outline_approximate()
outline_curvature_range_ratio()
outline_resample()
outline_smooth_samples()
outline_smooth_step()
outline_use_dft()
output_annotations()
output_centered()
output_csv_decimals()
output_default_options()
output_dir()
output_format()
output_frame_window()
output_graphs()
output_heatmaps()
output_image_per_tracklet()
output_interpolate_positions()
output_invalid_value()
output_min_frames()
output_normalize_midline_data()
output_posture_data()
output_prefix()
output_recognition_data()
output_statistics()
panic_button()
peak_mode()
posture_closing_size()
posture_closing_steps()
posture_direction_smoothing()
posture_head_percentage()
postures_per_thread()
python_path()
quit_after_average()
recognition_border()
recognition_border_shrink_percent()
recognition_border_size_rescale()
recognition_coeff()
recognition_enable()
recognition_image_scale()
recognition_image_size()
recognition_normalization()
recognition_save_progress_images()
recognition_save_training_images()
recognition_segment_add_factor()
recognition_shapes()
recognition_smooth_amount()
recording()
reset_average()
save_raw_movie()
settings_file()
smooth_window()
solid_background_color()
speed_extrapolation()
stop_after_minutes()
system_memory_limit()
tags_approximation()
tags_debug()
tags_dont_track()
tags_enable()
tags_equalize_hist()
tags_image_size()
tags_maximum_image_size()
tags_model_path()
tags_num_sides()
tags_path()
tags_recognize()
tags_save_predictions()
tags_saved_only()
tags_size_range()
tags_threshold()
terminate()
terminate_error()
terminate_training()
test_image()
tgrabs_use_threads()
threshold()
threshold_maximum()
threshold_ratio_range()
track_consistent_categories()
track_do_history_split()
track_end_segment_for_speed()
track_ignore()
track_include()
track_intensity_range()
track_max_individuals()
track_max_reassign_time()
track_max_speed()
track_only_categories()
track_posture_threshold()
track_segment_max_length()
track_speed_decay()
track_threshold()
track_threshold_2()
track_time_probability_enabled()
track_trusted_probability()
tracklet_export_difference_images()
tracklet_max_images()
tracklet_normalize_orientation()
use_adaptive_threshold()
use_closing()
use_differences()
version()
video_conversion_range()
video_info()
video_length()
video_reading_use_threads()
video_size()
video_source()
visual_field_eye_offset()
visual_field_eye_separation()
visual_field_history_smoothing()
visual_identification_version()
web_quality()
web_time_threshold()
C
calculate_posture()
built-in function
cam_circle_mask()
built-in function
cam_framerate()
built-in function
cam_limit_exposure()
built-in function
cam_matrix()
built-in function
cam_resolution()
built-in function
cam_scale()
built-in function
cam_undistort()
built-in function
cam_undistort_vector()
built-in function
categories_min_sample_images()
built-in function
categories_ordered()
built-in function
closing_size()
built-in function
cm_per_pixel()
built-in function
cmd_line()
built-in function
color_channel()
built-in function
correct_illegal_lines()
built-in function
correct_luminance()
built-in function
crop_offsets()
built-in function
crop_window()
built-in function
D
debug()
built-in function
debug_recognition_output_all_methods()
built-in function
dilation_size()
built-in function
E
enable_absolute_difference()
built-in function
enable_closed_loop()
built-in function
enable_difference()
built-in function
enable_live_tracking()
built-in function
equalize_histogram()
built-in function
error_terminate()
built-in function
event_min_peak_offset()
built-in function
exec()
built-in function
F
ffmpeg_crf()
built-in function
ffmpeg_path()
built-in function
filename()
built-in function
fishdata_dir()
built-in function
frame_rate()
built-in function
G
gpu_accepted_uniqueness()
built-in function
gpu_accumulation_enable_final_step()
built-in function
gpu_accumulation_max_segments()
built-in function
gpu_enable_accumulation()
built-in function
gpu_learning_rate()
built-in function
gpu_max_cache()
built-in function
gpu_max_epochs()
built-in function
gpu_max_sample_gb()
built-in function
gpu_min_elements()
built-in function
gpu_min_iterations()
built-in function
gpu_verbosity()
built-in function
grabber_force_settings()
built-in function
grid_points()
built-in function
grid_points_scaling()
built-in function
gui_auto_scale()
built-in function
gui_auto_scale_focus_one()
built-in function
gui_background_color()
built-in function
gui_connectivity_matrix()
built-in function
gui_connectivity_matrix_file()
built-in function
gui_draw_only_filtered_out()
built-in function
gui_equalize_blob_histograms()
built-in function
gui_faded_brightness()
built-in function
gui_fish_color()
built-in function
gui_focus_group()
built-in function
gui_foi_name()
built-in function
gui_foi_types()
built-in function
gui_frame()
built-in function
gui_happy_mode()
built-in function
gui_highlight_categories()
built-in function
gui_interface_scale()
built-in function
gui_max_path_time()
built-in function
gui_mode()
built-in function
gui_outline_thickness()
built-in function
gui_playback_speed()
built-in function
gui_recording_format()
built-in function
gui_run()
built-in function
gui_show_blobs()
built-in function
gui_show_boundary_crossings()
built-in function
gui_show_cliques()
built-in function
gui_show_dataset()
built-in function
gui_show_detailed_probabilities()
built-in function
gui_show_export_options()
built-in function
gui_show_fish()
built-in function
gui_show_graph()
built-in function
gui_show_heatmap()
built-in function
gui_show_histograms()
built-in function
gui_show_inactive_individuals()
built-in function
gui_show_match_modes()
built-in function
gui_show_memory_stats()
built-in function
gui_show_midline()
built-in function
gui_show_midline_histogram()
built-in function
gui_show_number_individuals()
built-in function
gui_show_only_unassigned()
built-in function
gui_show_outline()
built-in function
gui_show_paths()
built-in function
gui_show_pixel_grid()
built-in function
gui_show_posture()
built-in function
gui_show_probabilities()
built-in function
gui_show_recognition_bounds()
built-in function
gui_show_recognition_summary()
built-in function
gui_show_selections()
built-in function
gui_show_shadows()
built-in function
gui_show_texts()
built-in function
gui_show_uniqueness()
built-in function
gui_show_visualfield()
built-in function
gui_show_visualfield_ts()
built-in function
gui_single_identity_color()
built-in function
gui_timeline_alpha()
built-in function
gui_transparent_background()
built-in function
gui_zoom_limit()
built-in function
H
heatmap_dynamic()
built-in function
heatmap_frames()
built-in function
heatmap_ids()
built-in function
heatmap_normalization()
built-in function
heatmap_resolution()
built-in function
heatmap_smooth()
built-in function
heatmap_source()
built-in function
heatmap_value_range()
built-in function
history_matching_log()
built-in function
httpd_accepted_ip()
built-in function
httpd_port()
built-in function
huge_timestamp_ends_segment()
built-in function
huge_timestamp_seconds()
built-in function
I
image_adjust()
built-in function
image_brightness_increase()
built-in function
image_contrast_increase()
built-in function
image_invert()
built-in function
image_square_brightness()
built-in function
individual_names()
built-in function
individual_prefix()
built-in function
individuals_per_thread()
built-in function
L
limit()
built-in function
log_file()
built-in function
M
manual_identities()
built-in function
manual_matches()
built-in function
manual_splits()
built-in function
manually_approved()
built-in function
mask_path()
built-in function
match_mode()
built-in function
matching_probability_threshold()
built-in function
meta_age_days()
built-in function
meta_build()
built-in function
meta_cmd()
built-in function
meta_conditions()
built-in function
meta_conversion_time()
built-in function
meta_mass_mg()
built-in function
meta_misc()
built-in function
meta_real_width()
built-in function
meta_source_path()
built-in function
meta_species()
built-in function
meta_write_these()
built-in function
midline_invert()
built-in function
midline_resolution()
built-in function
midline_samples()
built-in function
midline_start_with_head()
built-in function
midline_stiff_percentage()
built-in function
midline_walk_offset()
built-in function
N
nowindow()
built-in function
,
[1]
O
outline_approximate()
built-in function
outline_curvature_range_ratio()
built-in function
outline_resample()
built-in function
outline_smooth_samples()
built-in function
outline_smooth_step()
built-in function
outline_use_dft()
built-in function
output_annotations()
built-in function
output_centered()
built-in function
output_csv_decimals()
built-in function
output_default_options()
built-in function
output_dir()
built-in function
output_format()
built-in function
output_frame_window()
built-in function
output_graphs()
built-in function
output_heatmaps()
built-in function
output_image_per_tracklet()
built-in function
output_interpolate_positions()
built-in function
output_invalid_value()
built-in function
output_min_frames()
built-in function
output_normalize_midline_data()
built-in function
output_posture_data()
built-in function
output_prefix()
built-in function
output_recognition_data()
built-in function
output_statistics()
built-in function
P
panic_button()
built-in function
peak_mode()
built-in function
posture_closing_size()
built-in function
posture_closing_steps()
built-in function
posture_direction_smoothing()
built-in function
posture_head_percentage()
built-in function
postures_per_thread()
built-in function
python_path()
built-in function
Q
quit_after_average()
built-in function
R
recognition_border()
built-in function
recognition_border_shrink_percent()
built-in function
recognition_border_size_rescale()
built-in function
recognition_coeff()
built-in function
recognition_enable()
built-in function
recognition_image_scale()
built-in function
recognition_image_size()
built-in function
recognition_normalization()
built-in function
recognition_save_progress_images()
built-in function
recognition_save_training_images()
built-in function
recognition_segment_add_factor()
built-in function
recognition_shapes()
built-in function
recognition_smooth_amount()
built-in function
recording()
built-in function
reset_average()
built-in function
S
save_raw_movie()
built-in function
settings_file()
built-in function
smooth_window()
built-in function
solid_background_color()
built-in function
speed_extrapolation()
built-in function
stop_after_minutes()
built-in function
system_memory_limit()
built-in function
T
tags_approximation()
built-in function
tags_debug()
built-in function
tags_dont_track()
built-in function
tags_enable()
built-in function
tags_equalize_hist()
built-in function
tags_image_size()
built-in function
tags_maximum_image_size()
built-in function
tags_model_path()
built-in function
tags_num_sides()
built-in function
tags_path()
built-in function
tags_recognize()
built-in function
tags_save_predictions()
built-in function
tags_saved_only()
built-in function
tags_size_range()
built-in function
tags_threshold()
built-in function
terminate()
built-in function
terminate_error()
built-in function
terminate_training()
built-in function
test_image()
built-in function
tgrabs_use_threads()
built-in function
threshold()
built-in function
threshold_maximum()
built-in function
threshold_ratio_range()
built-in function
track_consistent_categories()
built-in function
track_do_history_split()
built-in function
track_end_segment_for_speed()
built-in function
track_ignore()
built-in function
track_include()
built-in function
track_intensity_range()
built-in function
track_max_individuals()
built-in function
track_max_reassign_time()
built-in function
track_max_speed()
built-in function
track_only_categories()
built-in function
track_posture_threshold()
built-in function
track_segment_max_length()
built-in function
track_speed_decay()
built-in function
track_threshold()
built-in function
track_threshold_2()
built-in function
track_time_probability_enabled()
built-in function
track_trusted_probability()
built-in function
tracklet_export_difference_images()
built-in function
tracklet_max_images()
built-in function
tracklet_normalize_orientation()
built-in function
U
use_adaptive_threshold()
built-in function
use_closing()
built-in function
use_differences()
built-in function
V
version()
built-in function
video_conversion_range()
built-in function
video_info()
built-in function
video_length()
built-in function
video_reading_use_threads()
built-in function
video_size()
built-in function
video_source()
built-in function
visual_field_eye_offset()
built-in function
visual_field_eye_separation()
built-in function
visual_field_history_smoothing()
built-in function
visual_identification_version()
built-in function
W
web_quality()
built-in function
web_time_threshold()
built-in function