Index

_

_match() (rtcog.matching.matcher.Matcher method)

_start_time (rtcog.utils.core.SharedClock attribute)

A

action_end (rtcog.utils.sync.SyncEvents attribute) action_offsets (rtcog.utils.sync.ActionState attribute)

action_onsets (rtcog.utils.sync.ActionState attribute) action_state (rtcog.viz.esam_streaming.ESAMStreamer property) ActionState (class in rtcog.utils.sync)

B

BaseGUI (class in rtcog.gui.base_gui) BasicGUI (class in rtcog.gui.basic_gui)

BasicProcessor (class in rtcog.processor.basic_processor) buffer (rtcog.preproc.helpers.preproc_utils.CircularBuffer attribute) build_steps() (rtcog.preproc.pipeline.Pipeline method)

C

calculate_enorm_diff() (rtcog.matching.hit_detector.HitDetector method) calculate_spc() (in module rtcog.preproc.helpers.preproc_utils) CircularBuffer (class in rtcog.preproc.helpers.preproc_utils) cleanup() (rtcog.utils.shared_memory_manager.SharedMemoryManager method) cleanup_shared_memory() (rtcog.matching.matcher.Matcher method), [1] close() (rtcog.utils.recorder.RecordingFile method) (rtcog.viz.map_plotter.MapPlotter method) (rtcog.viz.plotter.Plotter method) (rtcog.viz.score_plotter.ScorePlotter method)

close_psychopy_window() (rtcog.gui.base_gui.BaseGUI method) (rtcog.gui.basic_gui.BasicGUI method) comm_process() (in module rtcog.comm.comm_process) compute_TR_data() (rtcog.processor.basic_processor.BasicProcessor method) (rtcog.processor.esam_processor.ESAMProcessor method) cooldown_end (rtcog.utils.sync.ActionState attribute) create_sync_events() (in module rtcog.utils.core) CustomReceiverInterface (class in rtcog.comm.receiver_interface)

D

Data_FromAFNI (rtcog.preproc.pipeline.Pipeline attribute) data_key (rtcog.viz.map_plotter.MapPlotter attribute) (rtcog.viz.plotter.Plotter attribute), [1] (rtcog.viz.response_plotter.ResponsePlotter attribute) (rtcog.viz.score_plotter.ScorePlotter attribute) data_out (rtcog.preproc.preproc_steps.PreprocStep attribute) Data_processed (rtcog.preproc.pipeline.Pipeline attribute)

detect() (rtcog.matching.hit_detector.HitDetector method) do_mot (rtcog.matching.hit_opts.HitOpts attribute) draw_ack_recording_screen() (rtcog.gui.esam_gui.EsamGUI method) draw_likert_instructions() (rtcog.gui.esam_gui.EsamGUI method) draw_likert_questions() (rtcog.gui.esam_gui.EsamGUI method) draw_resting_screen() (rtcog.gui.base_gui.BaseGUI method) (rtcog.gui.basic_gui.BasicGUI method)

E

EMA (rtcog.preproc.step_types.StepType attribute) EMAStep (class in rtcog.preproc.preproc_steps) end (rtcog.utils.sync.SyncEvents attribute) end_run() (rtcog.processor.basic_processor.BasicProcessor method) (rtcog.processor.esam_processor.ESAMProcessor method)

end_step() (rtcog.preproc.preproc_steps.KalmanStep method) (rtcog.preproc.preproc_steps.PreprocStep method) EsamGUI (class in rtcog.gui.esam_gui) ESAMProcessor (class in rtcog.processor.esam_processor) ESAMStreamer (class in rtcog.viz.esam_streaming)

F

file_exists() (in module rtcog.utils.core) final_steps() (rtcog.preproc.pipeline.Pipeline method) from_cli() (rtcog.utils.options.Options class method)

from_name() (rtcog.matching.matcher.Matcher class method) (rtcog.matching.matcher.Matcher method) from_yaml() (rtcog.utils.options.Options class method) full (rtcog.preproc.helpers.preproc_utils.CircularBuffer attribute)

G

gen_polort_regressors() (in module rtcog.preproc.helpers.preproc_utils) get_avail_keyboards() (in module rtcog.gui.gui_utils) get_callback() (rtcog.utils.recorder.RecordingFile method) get_class() (rtcog.preproc.preproc_steps.PreprocStep class method)

get_enabled_step_config() (rtcog.processor.esam_processor.ESAMProcessor method) get_experiment_info() (in module rtcog.gui.gui_utils) get_logger() (in module rtcog.utils.log) get_opts() (in module rtcog.hardware_tests.hardware_utils)

H

hit (rtcog.utils.sync.ActionState attribute) (rtcog.utils.sync.SyncEvents attribute) hit_thr (rtcog.matching.hit_opts.HitOpts attribute) (rtcog.viz.streaming_config.StreamingConfig attribute)

HitDetector (class in rtcog.matching.hit_detector) HitOpts (class in rtcog.matching.hit_opts) hits (rtcog.processor.esam_processor.ESAMProcessor attribute)

I

iGLM (class in rtcog.preproc.helpers.iglm) IGLM (rtcog.preproc.step_types.StepType attribute) iGLMStep (class in rtcog.preproc.preproc_steps) in_action (rtcog.utils.sync.ActionState attribute) in_cooldown (rtcog.utils.sync.ActionState attribute) (rtcog.viz.esam_streaming.ESAMStreamer property)

initialize_kalman_pool() (rtcog.preproc.helpers.kalman_filter.KalmanFilter method) initialize_pool() (rtcog.preproc.helpers.kalman_filter.KalmanFilter method) insert_idx (rtcog.preproc.helpers.preproc_utils.CircularBuffer attribute) is_hit() (rtcog.matching.hit_detector.HitDetector method)

K

KALMAN (rtcog.preproc.step_types.StepType attribute) kalman_filter_mv() (rtcog.preproc.helpers.kalman_filter.KalmanFilter static method)

KalmanFilter (class in rtcog.preproc.helpers.kalman_filter) KalmanStep (class in rtcog.preproc.preproc_steps)

L

lastaction_endTR (rtcog.processor.esam_processor.ESAMProcessor attribute)

load_fMRI_file() (in module rtcog.utils.fMRI) load_yaml() (rtcog.utils.options.Options static method)

M

main() (in module rtcog.matching.transcribe) (in module rtcog.run_minimal) MapPlotter (class in rtcog.viz.map_plotter) mask_fMRI_img() (in module rtcog.utils.fMRI) mask_img (rtcog.preproc.pipeline.Pipeline attribute) (rtcog.viz.streaming_config.StreamingConfig attribute) mask_Nv (rtcog.preproc.pipeline.Pipeline attribute) MaskMatcher (class in rtcog.matching.matcher) match() (rtcog.matching.matcher.Matcher method), [1] match_method (rtcog.matching.matching_opts.MatchingOpts attribute) match_start (rtcog.matching.matcher.Matcher attribute) (rtcog.matching.matching_opts.MatchingOpts attribute) Matcher (class in rtcog.matching.matcher) matcher (rtcog.processor.esam_processor.ESAMProcessor attribute) matching_opts (rtcog.viz.streaming_config.StreamingConfig attribute) MatchingOpts (class in rtcog.matching.matching_opts) MinimalReceiverInterface (class in rtcog.comm.receiver_interface) module rtcog.comm rtcog.comm.comm_process rtcog.comm.receiver_interface rtcog.controller rtcog.gui rtcog.gui.base_gui rtcog.gui.basic_gui rtcog.gui.esam_gui rtcog.gui.gui_utils rtcog.hardware_tests rtcog.hardware_tests.hardware_utils rtcog.matching rtcog.matching.hit_detector rtcog.matching.hit_opts rtcog.matching.matcher rtcog.matching.matching_opts rtcog.matching.matching_utils rtcog.matching.transcribe rtcog.paths rtcog.preproc rtcog.preproc.helpers rtcog.preproc.helpers.iglm rtcog.preproc.helpers.kalman_filter rtcog.preproc.helpers.preproc_utils rtcog.preproc.pipeline rtcog.preproc.preproc_steps rtcog.preproc.step_types rtcog.processor rtcog.processor.basic_processor rtcog.processor.esam_processor rtcog.run_minimal rtcog.utils rtcog.utils.core rtcog.utils.exceptions rtcog.utils.fMRI rtcog.utils.log rtcog.utils.options rtcog.utils.recorder rtcog.utils.shared_memory_manager rtcog.utils.sync rtcog.viz rtcog.viz.esam_streaming rtcog.viz.map_plotter rtcog.viz.plotter rtcog.viz.response_plotter rtcog.viz.score_plotter rtcog.viz.streaming_config

mot_thr (rtcog.matching.hit_opts.HitOpts attribute) motion_estimates (rtcog.preproc.pipeline.Pipeline attribute) mp_end (rtcog.matching.matcher.Matcher attribute) mp_new_tr (rtcog.matching.matcher.Matcher attribute) mp_shm_ready (rtcog.matching.matcher.Matcher attribute)

N

name (rtcog.preproc.preproc_steps.PreprocStep property) nconsec_vols (rtcog.matching.hit_opts.HitOpts attribute) new_tr (rtcog.utils.sync.SyncEvents attribute) nonline (rtcog.matching.hit_opts.HitOpts attribute) now() (rtcog.utils.core.SharedClock method) Nt (rtcog.matching.matcher.Matcher attribute) (rtcog.preproc.pipeline.Pipeline attribute) (rtcog.preproc.preproc_steps.PreprocStep attribute) (rtcog.viz.streaming_config.StreamingConfig attribute)

Ntemplates (rtcog.matching.matcher.Matcher attribute) Nv (rtcog.preproc.pipeline.Pipeline attribute) (rtcog.preproc.preproc_steps.PreprocStep attribute) (rtcog.viz.streaming_config.StreamingConfig attribute)

O

open() (rtcog.utils.recorder.Recorder method) (rtcog.utils.shared_memory_manager.SharedMemoryManager method) Options (class in rtcog.utils.options)

out_dir (rtcog.preproc.pipeline.Pipeline attribute) (rtcog.viz.streaming_config.StreamingConfig attribute) out_prefix (rtcog.preproc.pipeline.Pipeline attribute) (rtcog.viz.streaming_config.StreamingConfig attribute)

P

parse_cli_args() (rtcog.utils.options.Options class method) Pipeline (class in rtcog.preproc.pipeline) Plotter (class in rtcog.viz.plotter) poll_trigger() (rtcog.gui.base_gui.BaseGUI method) (rtcog.gui.basic_gui.BasicGUI method) PreprocStep (class in rtcog.preproc.preproc_steps)

process() (rtcog.preproc.pipeline.Pipeline method) process_first_volume() (rtcog.preproc.pipeline.Pipeline method) process_one_run() (rtcog.comm.receiver_interface.CustomReceiverInterface method) process_one_TR() (rtcog.comm.receiver_interface.CustomReceiverInterface method) (rtcog.comm.receiver_interface.MinimalReceiverInterface method) processed_tr (rtcog.preproc.pipeline.Pipeline attribute) (rtcog.preproc.pipeline.Pipeline property)

R

record() (rtcog.utils.recorder.RecordingFile method) record_oral_descr() (rtcog.gui.esam_gui.EsamGUI method) Recorder (class in rtcog.utils.recorder) RecordingFile (class in rtcog.utils.recorder) registry (rtcog.matching.matcher.Matcher attribute), [1] (rtcog.preproc.preproc_steps.PreprocStep attribute), [1] regress_vol() (rtcog.preproc.helpers.iglm.iGLM method) render_static() (rtcog.viz.score_plotter.ScorePlotter method) ResponsePlotter (class in rtcog.viz.response_plotter) rt_maskscore_vol() (in module rtcog.matching.matching_utils) rt_smooth_vol() (in module rtcog.preproc.helpers.preproc_utils) rt_svrscore_vol() (in module rtcog.matching.matching_utils) rtcog.comm module rtcog.comm.comm_process module rtcog.comm.receiver_interface module rtcog.controller module rtcog.gui module rtcog.gui.base_gui module rtcog.gui.basic_gui module rtcog.gui.esam_gui module rtcog.gui.gui_utils module rtcog.hardware_tests module rtcog.hardware_tests.hardware_utils module rtcog.matching module rtcog.matching.hit_detector module rtcog.matching.hit_opts module rtcog.matching.matcher module rtcog.matching.matching_opts module rtcog.matching.matching_utils module rtcog.matching.transcribe module rtcog.paths module rtcog.preproc module rtcog.preproc.helpers module rtcog.preproc.helpers.iglm module

rtcog.preproc.helpers.kalman_filter module rtcog.preproc.helpers.preproc_utils module rtcog.preproc.pipeline module rtcog.preproc.preproc_steps module rtcog.preproc.step_types module rtcog.processor module rtcog.processor.basic_processor module rtcog.processor.esam_processor module rtcog.run_minimal module rtcog.utils module rtcog.utils.core module rtcog.utils.exceptions module rtcog.utils.fMRI module rtcog.utils.log module rtcog.utils.options module rtcog.utils.recorder module rtcog.utils.shared_memory_manager module rtcog.utils.sync module rtcog.viz module rtcog.viz.esam_streaming module rtcog.viz.map_plotter module rtcog.viz.plotter module rtcog.viz.response_plotter module rtcog.viz.score_plotter module rtcog.viz.streaming_config module run() (rtcog.preproc.preproc_steps.PreprocStep method) (rtcog.viz.esam_streaming.ESAMStreamer method) run_full_action() (rtcog.gui.esam_gui.EsamGUI method) run_funcs (rtcog.preproc.pipeline.Pipeline attribute) run_streamer() (in module rtcog.viz.esam_streaming) run_volume() (rtcog.preproc.helpers.kalman_filter.KalmanFilter method)

S

save (rtcog.preproc.preproc_steps.PreprocStep attribute) save_config() (rtcog.utils.options.Options method) save_likert_files() (rtcog.gui.esam_gui.EsamGUI method) save_motion_estimates() (rtcog.preproc.pipeline.Pipeline method) save_nifti() (rtcog.preproc.preproc_steps.PreprocStep method) save_nifti_files() (rtcog.preproc.pipeline.Pipeline method) save_orig (rtcog.preproc.pipeline.Pipeline attribute) save_timing() (rtcog.comm.receiver_interface.CustomReceiverInterface method) save_trigger() (rtcog.gui.base_gui.BaseGUI method) (rtcog.gui.basic_gui.BasicGUI method) ScorePlotter (class in rtcog.viz.score_plotter) scores (rtcog.matching.matcher.Matcher attribute) server_ready (rtcog.utils.sync.SyncEvents attribute) set_logger() (in module rtcog.utils.log) setup_afni() (in module rtcog.utils.core) setup_shared_memory() (rtcog.matching.matcher.Matcher method), [1] shared_action_offsets (rtcog.processor.esam_processor.ESAMProcessor attribute) shared_action_onsets (rtcog.processor.esam_processor.ESAMProcessor attribute) shared_tr_data (rtcog.processor.esam_processor.ESAMProcessor attribute) SharedClock (class in rtcog.utils.core) SharedMemoryManager (class in rtcog.utils.shared_memory_manager)

shm_ready (rtcog.utils.sync.SyncEvents attribute) should_update() (rtcog.viz.map_plotter.MapPlotter method) (rtcog.viz.plotter.Plotter method) (rtcog.viz.response_plotter.ResponsePlotter method) size (rtcog.preproc.helpers.preproc_utils.CircularBuffer attribute) SMOOTH (rtcog.preproc.step_types.StepType attribute) SmoothStep (class in rtcog.preproc.preproc_steps) snapshot (rtcog.preproc.pipeline.Pipeline attribute) snapshot() (rtcog.preproc.preproc_steps.PreprocStep method) SNORM (rtcog.preproc.step_types.StepType attribute) SnormStep (class in rtcog.preproc.preproc_steps) start_recording() (rtcog.utils.recorder.RecordingFile method) start_step() (rtcog.preproc.preproc_steps.PreprocStep method) start_streaming() (rtcog.processor.esam_processor.ESAMProcessor method) steps (rtcog.preproc.pipeline.Pipeline attribute) StepType (class in rtcog.preproc.step_types) stop_recording() (rtcog.utils.recorder.RecordingFile method) StreamingConfig (class in rtcog.viz.streaming_config) suffix (rtcog.preproc.preproc_steps.PreprocStep attribute) SVRMatcher (class in rtcog.matching.matcher) SyncEvents (class in rtcog.utils.sync)

T

template_labels (rtcog.viz.streaming_config.StreamingConfig attribute) TnormStep (class in rtcog.preproc.preproc_steps)

tr_index (rtcog.utils.sync.SyncEvents attribute) transcribe() (in module rtcog.matching.transcribe)

U

unmask_fMRI_img() (in module rtcog.utils.fMRI) update() (rtcog.preproc.helpers.preproc_utils.CircularBuffer method) (rtcog.viz.esam_streaming.ESAMStreamer method) (rtcog.viz.map_plotter.MapPlotter method) (rtcog.viz.plotter.Plotter method) (rtcog.viz.response_plotter.ResponsePlotter method) (rtcog.viz.score_plotter.ScorePlotter method)

update_welford() (rtcog.preproc.helpers.kalman_filter.KalmanFilter method)

V

validate_likert_questions() (in module rtcog.gui.gui_utils)

vols_noaction (rtcog.matching.matching_opts.MatchingOpts attribute) VolumeOverflowError

W

welford() (in module rtcog.preproc.helpers.preproc_utils) WINDOWING (rtcog.preproc.step_types.StepType attribute) WindowingStep (class in rtcog.preproc.preproc_steps)

write_action() (rtcog.processor.esam_processor.ESAMProcessor method) write_hit_arrays() (rtcog.processor.esam_processor.ESAMProcessor method) write_hit_maps() (rtcog.processor.esam_processor.ESAMProcessor method) write_report() (rtcog.processor.esam_processor.ESAMProcessor method)