rtcog package

Subpackages

• rtcog.comm package
  • Submodules
  • rtcog.comm.comm_process module
    • comm_process()
  • rtcog.comm.receiver_interface module
    • CustomReceiverInterface
      • CustomReceiverInterface.process_one_TR()
      • CustomReceiverInterface.process_one_run()
      • CustomReceiverInterface.save_timing()
    • MinimalReceiverInterface
      • MinimalReceiverInterface.process_one_TR()
  • Module contents
• rtcog.processor package
  • Submodules
  • rtcog.processor.basic_processor module
    • BasicProcessor
      • BasicProcessor.compute_TR_data()
      • BasicProcessor.end_run()
  • rtcog.processor.esam_processor module
    • ESAMProcessor
      • ESAMProcessor.lastaction_endTR
      • ESAMProcessor.matcher
      • ESAMProcessor.shared_tr_data
      • ESAMProcessor.shared_action_onsets
      • ESAMProcessor.shared_action_offsets
      • ESAMProcessor.hits
      • ESAMProcessor.compute_TR_data()
      • ESAMProcessor.end_run()
      • ESAMProcessor.get_enabled_step_config()
      • ESAMProcessor.start_streaming()
      • ESAMProcessor.write_action()
      • ESAMProcessor.write_hit_arrays()
      • ESAMProcessor.write_hit_maps()
      • ESAMProcessor.write_report()
  • Module contents
• rtcog.preproc package
  • Subpackages
    • rtcog.preproc.helpers package
      • Submodules
      • rtcog.preproc.helpers.iglm module
      • rtcog.preproc.helpers.kalman_filter module
      • rtcog.preproc.helpers.preproc_utils module
      • Module contents
  • Submodules
  • rtcog.preproc.pipeline module
    • Pipeline
      • Pipeline.Nt
      • Pipeline.mask_Nv
      • Pipeline.mask_img
      • Pipeline.Nv
      • Pipeline.steps
      • Pipeline.run_funcs
      • Pipeline.motion_estimates
      • Pipeline.Data_FromAFNI
      • Pipeline.Data_processed
      • Pipeline.processed_tr
      • Pipeline.out_dir
      • Pipeline.out_prefix
      • Pipeline.save_orig
      • Pipeline.snapshot
      • Pipeline.build_steps()
      • Pipeline.final_steps()
      • Pipeline.process()
      • Pipeline.process_first_volume()
      • Pipeline.processed_tr
      • Pipeline.save_motion_estimates()
      • Pipeline.save_nifti_files()
  • rtcog.preproc.preproc_steps module
    • EMAStep
    • KalmanStep
      • KalmanStep.end_step()
    • PreprocStep
      • PreprocStep.save
      • PreprocStep.suffix
      • PreprocStep.Nv
      • PreprocStep.Nt
      • PreprocStep.data_out
      • PreprocStep.registry
      • PreprocStep.end_step()
      • PreprocStep.get_class()
      • PreprocStep.name
      • PreprocStep.registry
      • PreprocStep.run()
      • PreprocStep.save_nifti()
      • PreprocStep.snapshot()
      • PreprocStep.start_step()
    • SmoothStep
    • SnormStep
    • TnormStep
    • WindowingStep
    • iGLMStep
  • rtcog.preproc.step_types module
    • StepType
      • StepType.EMA
      • StepType.IGLM
      • StepType.KALMAN
      • StepType.SMOOTH
      • StepType.SNORM
      • StepType.WINDOWING
  • Module contents
• rtcog.matching package
  • Submodules
  • rtcog.matching.hit_detector module
    • HitDetector
      • HitDetector.calculate_enorm_diff()
      • HitDetector.detect()
      • HitDetector.is_hit()
  • rtcog.matching.hit_opts module
    • HitOpts
      • HitOpts.do_mot
      • HitOpts.hit_thr
      • HitOpts.mot_thr
      • HitOpts.nconsec_vols
      • HitOpts.nonline
  • rtcog.matching.matcher module
    • MaskMatcher
    • Matcher
      • Matcher.registry
      • Matcher.match_start
      • Matcher.Nt
      • Matcher.scores
      • Matcher.Ntemplates
      • Matcher.mp_end
      • Matcher.mp_new_tr
      • Matcher.mp_shm_ready
      • Matcher.from_name()
      • Matcher.match()
      • Matcher.setup_shared_memory()
      • Matcher.cleanup_shared_memory()
      • Matcher._match()
      • Matcher.cleanup_shared_memory()
      • Matcher.from_name()
      • Matcher.match()
      • Matcher.registry
      • Matcher.setup_shared_memory()
    • SVRMatcher
  • rtcog.matching.matching_opts module
    • MatchingOpts
      • MatchingOpts.match_method
      • MatchingOpts.match_start
      • MatchingOpts.vols_noaction
  • rtcog.matching.matching_utils module
    • rt_maskscore_vol()
    • rt_svrscore_vol()
  • rtcog.matching.transcribe module
    • main()
    • transcribe()
  • Module contents
• rtcog.viz package
  • Submodules
  • rtcog.viz.esam_streaming module
    • ESAMStreamer
      • ESAMStreamer.action_state
      • ESAMStreamer.in_cooldown
      • ESAMStreamer.run()
      • ESAMStreamer.update()
    • run_streamer()
  • rtcog.viz.map_plotter module
    • MapPlotter
      • MapPlotter.close()
      • MapPlotter.data_key
      • MapPlotter.should_update()
      • MapPlotter.update()
  • rtcog.viz.plotter module
    • Plotter
      • Plotter.data_key
      • Plotter.close()
      • Plotter.data_key
      • Plotter.should_update()
      • Plotter.update()
  • rtcog.viz.response_plotter module
    • ResponsePlotter
      • ResponsePlotter.data_key
      • ResponsePlotter.should_update()
      • ResponsePlotter.update()
  • rtcog.viz.score_plotter module
    • ScorePlotter
      • ScorePlotter.close()
      • ScorePlotter.data_key
      • ScorePlotter.render_static()
      • ScorePlotter.update()
  • rtcog.viz.streaming_config module
    • StreamingConfig
      • StreamingConfig.Nt
      • StreamingConfig.Nv
      • StreamingConfig.hit_thr
      • StreamingConfig.mask_img
      • StreamingConfig.matching_opts
      • StreamingConfig.out_dir
      • StreamingConfig.out_prefix
      • StreamingConfig.template_labels
  • Module contents
• rtcog.controller package
  • Submodules
  • rtcog.controller.action_series module
  • rtcog.controller.controller module
  • Module contents
• rtcog.gui package
  • Submodules
  • rtcog.gui.base_gui module
    • BaseGUI
      • BaseGUI.close_psychopy_window()
      • BaseGUI.draw_resting_screen()
      • BaseGUI.poll_trigger()
      • BaseGUI.save_trigger()
  • rtcog.gui.esam_gui module
    • EsamGUI
      • EsamGUI.draw_ack_recording_screen()
      • EsamGUI.draw_likert_instructions()
      • EsamGUI.draw_likert_questions()
      • EsamGUI.record_oral_descr()
      • EsamGUI.run_full_action()
      • EsamGUI.save_likert_files()
  • rtcog.gui.gui_utils module
    • get_avail_keyboards()
    • get_experiment_info()
    • validate_likert_questions()
  • rtcog.gui.preproc_gui module
    • BasicGUI
      • BasicGUI.close_psychopy_window()
      • BasicGUI.draw_resting_screen()
      • BasicGUI.poll_trigger()
      • BasicGUI.save_trigger()
  • Module contents
• rtcog.utils package
  • Submodules
  • rtcog.utils.core module
    • SharedClock
      • SharedClock._start_time
      • SharedClock.now()
    • create_sync_events()
    • file_exists()
    • setup_afni()
  • rtcog.utils.exceptions module
    • VolumeOverflowError
  • rtcog.utils.fMRI module
    • load_fMRI_file()
    • mask_fMRI_img()
    • unmask_fMRI_img()
  • rtcog.utils.log module
    • get_logger()
    • set_logger()
  • rtcog.utils.options module
    • Options
      • Options.from_cli()
      • Options.from_yaml()
      • Options.load_yaml()
      • Options.parse_cli_args()
      • Options.save_config()
  • rtcog.utils.recorder module
    • Recorder
      • Recorder.open()
    • RecordingFile
      • RecordingFile.close()
      • RecordingFile.get_callback()
      • RecordingFile.record()
      • RecordingFile.start_recording()
      • RecordingFile.stop_recording()
  • rtcog.utils.shared_memory_manager module
    • SharedMemoryManager
      • SharedMemoryManager.cleanup()
      • SharedMemoryManager.open()
  • rtcog.utils.sync module
    • ActionState
      • ActionState.action_offsets
      • ActionState.action_onsets
      • ActionState.cooldown_end
      • ActionState.hit
      • ActionState.in_action
      • ActionState.in_cooldown
    • SyncEvents
      • SyncEvents.action_end
      • SyncEvents.end
      • SyncEvents.hit
      • SyncEvents.new_tr
      • SyncEvents.server_ready
      • SyncEvents.shm_ready
      • SyncEvents.tr_index
  • Module contents
• rtcog.hardware_tests package
  • Submodules
  • rtcog.hardware_tests.hardware_utils module
    • get_opts()
  • rtcog.hardware_tests.test_scanner_latency module
  • Module contents

Submodules

rtcog.experiment_registry module

rtcog.main module

rtcog.paths module

Directory structure definitions for the rtcog software package.

This module defines key paths used throughout the codebase. All paths are constructed relative to the location of this file.

rtcog.run_minimal module

Minimal entry point for rtcog without GUI dependencies.

rtcog.run_minimal.main()

Module contents