Index

Symbols

--allocations slf-server-batches command line option --animal slf-manifest-print command line option --batch-id slf-server-batches command line option slf-server-retire-batch command line option --binarize slf-process-two-photon command line option --combine slf-process-two-photon command line option --dataset-name slf-forge command line option --dataset-path slf-dataset-state command line option slf-plan-dataset command line option --destination slf-server-pull command line option --drop-without-outcome slf-server-retire-batch command line option --end-time slf-server-print command line option --energy slf-process-video command line option --environment slf-server-configure command line option --force slf-omp command line option slf-server-retire-batch command line option --force-recreate slf-forge command line option --host slf-server-configure command line option --job-data slf-server-print command line option --job-id slf-forge command line option slf-process command line option slf-reset command line option slf-server-print command line option --no-progress slf-checksum command line option slf-forge command line option slf-manifest-create command line option slf-process command line option --notes slf-manifest-print command line option --password slf-server-configure command line option --pipeline slf-clean command line option slf-reset command line option --process slf-process-two-photon command line option --project slf-server-discover command line option --project-path slf-forge command line option slf-manifest command line option slf-plan-project command line option --queue slf-server-print command line option --recreate-animal slf-forge command line option --regenerate-checksum slf-checksum command line option --regenerate-plan slf-plan-dataset command line option slf-plan-session command line option --register slf-process-two-photon command line option --remote-path slf-server-pull command line option --root slf-server-configure command line option --session slf-forge command line option --session-path slf-checksum command line option slf-plan-session command line option slf-process command line option --source slf-omp command line option --start-time slf-server-print command line option --summary slf-manifest-print command line option --target slf-omp command line option --target-camera slf-process-video command line option --target-plane slf-process-two-photon command line option --timestamp slf-process-video command line option --track slf-process-video command line option --transport slf-mcp command line option --unit-path slf-clean command line option slf-reset command line option --user slf-server-print command line option --username slf-server-configure command line option

--workers slf-checksum command line option slf-forge command line option slf-process command line option --yes slf-omp command line option -a slf-manifest-print command line option slf-server-batches command line option -b slf-process-two-photon command line option slf-server-batches command line option slf-server-retire-batch command line option -cb slf-process-two-photon command line option -d slf-server-pull command line option -dn slf-forge command line option -do slf-server-retire-batch command line option -dp slf-dataset-state command line option slf-plan-dataset command line option -e slf-server-configure command line option -en slf-process-video command line option -et slf-server-print command line option -f slf-forge command line option slf-omp command line option slf-server-retire-batch command line option -h slf-server-configure command line option -id slf-forge command line option slf-process command line option slf-reset command line option slf-server-print command line option -j slf-server-print command line option -n slf-manifest-print command line option -np slf-checksum command line option slf-forge command line option slf-manifest-create command line option slf-process command line option -p slf-clean command line option slf-process-two-photon command line option slf-reset command line option slf-server-configure command line option slf-server-discover command line option -pp slf-forge command line option slf-manifest command line option slf-plan-project command line option -q slf-server-print command line option -r slf-process-two-photon command line option slf-server-configure command line option slf-server-pull command line option -ra slf-forge command line option -rc slf-checksum command line option -rp slf-plan-dataset command line option slf-plan-session command line option -s slf-forge command line option slf-manifest-print command line option slf-omp command line option -sp slf-checksum command line option slf-plan-session command line option slf-process command line option -st slf-server-print command line option -t slf-mcp command line option slf-omp command line option -tc slf-process-video command line option -tp slf-process-two-photon command line option -tr slf-process-video command line option -ts slf-process-video command line option -u slf-server-configure command line option slf-server-print command line option -up slf-clean command line option slf-reset command line option -w slf-checksum command line option slf-forge command line option slf-process command line option -y slf-omp command line option

_

_client (sollertia_forgery.server.Server attribute) _command (sollertia_forgery.server.Job attribute) _configuration (sollertia_forgery.server.Server attribute)

_data (sollertia_forgery.managing.ProjectManifest attribute) _open (sollertia_forgery.server.Server attribute) _server (sollertia_forgery.orchestration.RemoteHost attribute) _sftp (sollertia_forgery.server.Server attribute)

A

ABANDONED_ALLOCATION (in module sollertia_forgery.orchestration.remote) abort_job() (sollertia_forgery.server.Server method) abort_jobs() (sollertia_forgery.server.Server method) active_jobs (sollertia_forgery.orchestration.JobExecutionState attribute) add_command() (sollertia_forgery.server.Job method) all_jobs (sollertia_forgery.orchestration.JobExecutionState attribute) AllocationResolution (class in sollertia_forgery.orchestration)

animals (sollertia_forgery.managing.ProjectManifest property) assemble_mesoscope_session() (in module sollertia_forgery.mesoscope_vr) AssemblyGeometry (class in sollertia_forgery.shared_assets) AVAILABLE (sollertia_forgery.shared_assets.OpenMPStatus attribute) AVERSIVE_GUIDED (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) AWAITING_CLOSURE_BATCH (in module sollertia_forgery.orchestration.remote)

B

batch_directory (sollertia_forgery.orchestration.SubmissionBatch attribute) batch_directory() (in module sollertia_forgery.orchestration) batch_id (sollertia_forgery.orchestration.AllocationResolution attribute) (sollertia_forgery.orchestration.SubmissionBatch attribute) batch_ids (sollertia_forgery.orchestration.SubmissionBatch attribute) BATCH_PIPELINES (in module sollertia_forgery.orchestration.dispatch) batches (sollertia_forgery.orchestration.SubmissionLedger attribute) BINARIZE (sollertia_forgery.two_photon.SingleRecordingJobNames attribute) BLINKING_STATE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute)

BLOCKED (sollertia_forgery.server.JobStatus attribute) blocked_jobs (sollertia_forgery.orchestration.JobExecutionState attribute) BODY_CAMERA_FRAME_LUMINANCE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) BODY_CAMERA_MOTION_ENERGY (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) BOOT_FAIL (sollertia_forgery.server.JobStatus attribute) BRAKE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) build_pending_job() (in module sollertia_forgery.orchestration)

C

CAMERA_EXTRACTION_JOB_NAME (in module ataraxis_video_system.orchestration.jobs) cancel_allocations() (in module sollertia_forgery.orchestration) CANCEL_REMEDIATION (in module sollertia_forgery.orchestration.remote) cancel_submissions() (in module sollertia_forgery.orchestration) canceled (sollertia_forgery.orchestration.JobExecutionState attribute) (sollertia_forgery.orchestration.SchedulerReading attribute) canceling() (sollertia_forgery.orchestration.SchedulerReading method) CANCELLED (sollertia_forgery.server.JobStatus attribute) CHECKSUM (sollertia_forgery.shared_assets.ProcessingPipelines attribute) CHECKSUM_JOB_NAME (in module sollertia_forgery.managing.checksum) checksum_job_prerequisites() (in module sollertia_forgery.managing) claim_state (sollertia_forgery.orchestration.AllocationResolution attribute) classify_batch() (in module sollertia_forgery.orchestration) clean() (sollertia_forgery.orchestration.ExecutionHost method) (sollertia_forgery.orchestration.LocalHost static method) (sollertia_forgery.orchestration.RemoteHost method) clean_pipeline_output() (in module sollertia_forgery.orchestration) close() (sollertia_forgery.server.Server method)

close_batch() (in module sollertia_forgery.orchestration) close_covered_batches() (in module sollertia_forgery.orchestration) close_settled_batches() (in module sollertia_forgery.orchestration) COMBINE (sollertia_forgery.two_photon.SingleRecordingJobNames attribute) command_script (sollertia_forgery.server.Job property) COMPLETED (sollertia_forgery.server.JobStatus attribute) concurrency_limits (sollertia_forgery.orchestration.JobExecutionState attribute) concurrency_reservations (sollertia_forgery.orchestration.JobExecutionState attribute) connect_to_server() (in module sollertia_forgery.orchestration) CONTROLLER_EXTRACTION_JOB_NAME (in module ataraxis_communication_interface.orchestration.jobs) core_budget (sollertia_forgery.orchestration.JobExecutionState attribute) count_feather_rows() (in module sollertia_forgery.shared_assets) covered_batch_ids (sollertia_forgery.orchestration.SubmissionBatch property) create() (sollertia_forgery.server.Server method) create_server_configuration_file() (in module sollertia_forgery.server) CUE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) current_timestamp() (in module sollertia_forgery.orchestration)

D

data (sollertia_forgery.managing.ProjectManifest property) DATASET_STATE_FILENAME (in module sollertia_forgery.forging.state) dataset_state_path() (in module sollertia_forgery.forging) DATASET_UNIT (in module sollertia_forgery.orchestration.dispatch) DatasetColumn (class in sollertia_forgery.mesoscope_vr) (class in sollertia_forgery.mesoscope_vr.metadata) DEADLINE (sollertia_forgery.server.JobStatus attribute) define_dataset() (sollertia_forgery.orchestration.ExecutionHost method) (sollertia_forgery.orchestration.LocalHost static method) (sollertia_forgery.orchestration.RemoteHost method) define_forging_dataset() (in module sollertia_forgery.forging) delay_terminal() (in module sollertia_forgery.shared_assets) DILATION_STATE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute)

discover_checksum_jobs() (in module sollertia_forgery.managing) discover_forging_jobs() (in module sollertia_forgery.forging) discover_microcontroller_jobs() (in module sollertia_forgery.microcontrollers) discover_project_data() (in module sollertia_forgery.server) discover_project_datasets() (in module sollertia_forgery.forging) discover_project_markers() (in module sollertia_forgery.server) discover_runtime_jobs() (in module sollertia_forgery.runtime) discover_two_photon_jobs() (in module sollertia_forgery.two_photon) discover_video_jobs() (in module sollertia_forgery.video) dispatch_priorities (sollertia_forgery.orchestration.JobExecutionState attribute) DISTANCE_CM (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) DROP_REMEDIATION (in module sollertia_forgery.orchestration.remote)

E

ELAPSED_MINUTES (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) ENERGY_JOB_NAME (in module sollertia_forgery.video.pipeline) environment (sollertia_forgery.server.Server property) (sollertia_forgery.server.ServerConfiguration attribute) execute_command() (sollertia_forgery.server.Server method) ExecutionHost (class in sollertia_forgery.orchestration) executor_id (sollertia_forgery.orchestration.GenericPendingJob attribute) exists() (sollertia_forgery.server.Server method) EYE_CENTER_X_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute)

EYE_CENTER_Y_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) EYE_HEIGHT_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) EYE_OPENNESS (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) EYE_WIDTH_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute)

F

FACE_CAMERA_FRAME_LUMINANCE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) FACE_CAMERA_MOTION_ENERGY (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) FAILED (sollertia_forgery.server.JobStatus attribute) FAILED_ALLOCATION (in module sollertia_forgery.orchestration.remote) failed_job_keys (sollertia_forgery.orchestration.JobExecutionState attribute) fetch() (sollertia_forgery.orchestration.ExecutionHost method) (sollertia_forgery.orchestration.LocalHost static method) (sollertia_forgery.orchestration.RemoteHost method) find_paths() (sollertia_forgery.server.Server method)

FINISHED_ALLOCATION (in module sollertia_forgery.orchestration.remote) forget_batch_records() (in module sollertia_forgery.orchestration) forget_batches() (in module sollertia_forgery.orchestration) FORGING (sollertia_forgery.shared_assets.ProcessingPipelines attribute) forging_cross_recording_paths() (in module sollertia_forgery.forging) FORGING_JOB_CONCURRENCY_LIMITS (in module sollertia_forgery.forging.pipeline) FORGING_JOB_NAME (in module sollertia_forgery.forging.pipeline) forging_job_prerequisites() (in module sollertia_forgery.forging) forging_tracker_path() (in module sollertia_forgery.forging) ForgingAssembler (class in sollertia_forgery.registries) FRAME (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute)

G

generate_dataset_state() (in module sollertia_forgery.forging) generate_project_manifest() (in module sollertia_forgery.managing) generate_project_plan() (in module sollertia_forgery.orchestration) generate_state() (sollertia_forgery.orchestration.ExecutionHost method) (sollertia_forgery.orchestration.LocalHost static method) (sollertia_forgery.orchestration.RemoteHost method) GenericPendingJob (class in sollertia_forgery.orchestration) get_animal_for_session() (sollertia_forgery.managing.ProjectManifest method) get_blocked_job_ids() (sollertia_forgery.server.Server method) get_eligible_modules() (in module sollertia_forgery.mesoscope_vr)

get_job_status() (sollertia_forgery.server.Server method) get_job_statuses() (sollertia_forgery.server.Server method) get_module_event_codes() (in module sollertia_forgery.mesoscope_vr) get_queued_job_ids() (sollertia_forgery.server.Server method) get_server_configuration() (in module sollertia_forgery.server) get_server_configuration_path() (in module sollertia_forgery.server) get_session_data() (sollertia_forgery.managing.ProjectManifest method) get_sessions() (sollertia_forgery.managing.ProjectManifest method) get_system_for_session() (sollertia_forgery.managing.ProjectManifest method) GONE_ALLOCATION (in module sollertia_forgery.orchestration.remote) group_jobs_by_tracker() (in module sollertia_forgery.orchestration)

H

HELD_ALLOCATION (in module sollertia_forgery.orchestration.remote)

host (sollertia_forgery.server.Server property) (sollertia_forgery.server.ServerConfiguration attribute)

I

IN_TRIGGER_ZONE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute)

is_directory() (sollertia_forgery.server.Server method)

J

Job (class in sollertia_forgery.server) job_execution_manager() (in module sollertia_forgery.orchestration) job_id (sollertia_forgery.server.Job attribute)

job_name (sollertia_forgery.server.Job attribute) JobExecutionState (class in sollertia_forgery.orchestration) JobStatus (class in sollertia_forgery.server)

L

label (sollertia_forgery.orchestration.ExecutionHost property) (sollertia_forgery.orchestration.LocalHost property) (sollertia_forgery.orchestration.RemoteHost property) LICK (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) LINKED (sollertia_forgery.shared_assets.OpenMPStatus attribute)

list_directory() (sollertia_forgery.server.Server method) LOCAL_HOST_LABEL (in module sollertia_forgery.orchestration.reconcile) LocalHost (class in sollertia_forgery.orchestration) locate_mesoscope_pose_predictions() (in module sollertia_forgery.mesoscope_vr) locate_two_photon_data() (in module sollertia_forgery.mesoscope_vr) lock (sollertia_forgery.orchestration.JobExecutionState attribute)

M

manager_thread (sollertia_forgery.orchestration.JobExecutionState attribute) MANIFEST (sollertia_forgery.shared_assets.ProcessingPipelines attribute) MANIFEST_AXES (in module sollertia_forgery.managing.manifest) MANIFEST_JOB_NAME (in module sollertia_forgery.managing.manifest) MANIFEST_SEMI_FIELDS (in module sollertia_forgery.managing.manifest) materialize() (sollertia_forgery.orchestration.ExecutionHost method) (sollertia_forgery.orchestration.LocalHost class method) (sollertia_forgery.orchestration.RemoteHost method) memory_budget_mb (sollertia_forgery.orchestration.JobExecutionState attribute) merge_event_streams() (in module sollertia_forgery.shared_assets) MESOSCOPE_ADMISSION_PIPELINES (in module sollertia_forgery.mesoscope_vr.forging) MESOSCOPE_COLUMN_DESCRIPTIONS (in module sollertia_forgery.mesoscope_vr.metadata) MESOSCOPE_MULTI_RECORDING_SESSION_TYPES (in module sollertia_forgery.mesoscope_vr.two_photon) MICROCONTROLLER (sollertia_forgery.shared_assets.ProcessingPipelines attribute) microcontroller_job_prerequisites() (in module sollertia_forgery.microcontrollers) MicrocontrollerParser (class in sollertia_forgery.registries) MINIMUM_CHUNK_FRAMES (in module sollertia_forgery.video.motion_energy) module sollertia_forgery.forging sollertia_forgery.managing sollertia_forgery.mesoscope_vr sollertia_forgery.microcontrollers sollertia_forgery.orchestration sollertia_forgery.registries sollertia_forgery.runtime sollertia_forgery.server sollertia_forgery.shared_assets sollertia_forgery.two_photon sollertia_forgery.video

MULTI_DAY_CELL_FLUORESCENCE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) MULTI_DAY_NEUROPIL_FLUORESCENCE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) MULTI_DAY_SPIKES (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) MULTI_DAY_SUBTRACTED_FLUORESCENCE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) multi_recording_dataset_name() (in module sollertia_forgery.shared_assets) MULTIDAY_DISCOVERY_JOB_NAME (in module sollertia_forgery.forging.pipeline) MULTIDAY_EXTRACTION_JOB_NAME (in module sollertia_forgery.forging.pipeline)

N

name (sollertia_forgery.orchestration.GenericPendingJob attribute) natural_sort() (in module sollertia_forgery.shared_assets)

NO_REMEDIATION (in module sollertia_forgery.orchestration.remote) NODE_FAIL (sollertia_forgery.server.JobStatus attribute)

O

OpenMPStatus (class in sollertia_forgery.shared_assets) options (sollertia_forgery.orchestration.GenericPendingJob attribute)

OUT_OF_MEMORY (sollertia_forgery.server.JobStatus attribute) OUTCOME_FILE_SUFFIX (in module sollertia_forgery.orchestration.batches)

P

parse_brake() (in module sollertia_forgery.mesoscope_vr) parse_encoder() (in module sollertia_forgery.mesoscope_vr) parse_gas_puff() (in module sollertia_forgery.mesoscope_vr) PARSE_JOB_NAME (in module sollertia_forgery.microcontrollers.pipeline) parse_lick() (in module sollertia_forgery.mesoscope_vr) parse_mesoscope_frame() (in module sollertia_forgery.mesoscope_vr) parse_runtime() (in module sollertia_forgery.mesoscope_vr) parse_screen() (in module sollertia_forgery.mesoscope_vr) parse_torque() (in module sollertia_forgery.mesoscope_vr) parse_valve() (in module sollertia_forgery.mesoscope_vr) password (sollertia_forgery.server.ServerConfiguration attribute) PENDING (sollertia_forgery.server.JobStatus attribute) pending_jobs (sollertia_forgery.orchestration.JobExecutionState attribute) pipeline (sollertia_forgery.orchestration.GenericPendingJob attribute) pipelines (sollertia_forgery.orchestration.SubmissionBatch property) plan() (sollertia_forgery.orchestration.ExecutionHost method) (sollertia_forgery.orchestration.LocalHost static method) (sollertia_forgery.orchestration.RemoteHost method) pool_size (sollertia_forgery.orchestration.JobExecutionState attribute) posix_text() (in module sollertia_forgery.shared_assets) PREEMPTED (sollertia_forgery.server.JobStatus attribute) prepare_batch() (in module sollertia_forgery.orchestration) PREVIEWED (sollertia_forgery.shared_assets.OpenMPStatus attribute) prime_two_photon_recording() (in module sollertia_forgery.two_photon) print_data() (sollertia_forgery.managing.ProjectManifest method) print_notes() (sollertia_forgery.managing.ProjectManifest method) print_summary() (sollertia_forgery.managing.ProjectManifest method) PROCESS (sollertia_forgery.two_photon.SingleRecordingJobNames attribute) process_mesoscope_video_tracking() (in module sollertia_forgery.mesoscope_vr) ProcessingPipelines (class in sollertia_forgery.shared_assets) PROGRESSING_BATCH (in module sollertia_forgery.orchestration.remote) project_jobs_path() (in module sollertia_forgery.managing) project_manifest_path() (in module sollertia_forgery.managing) project_plan_path() (in module sollertia_forgery.orchestration) PROJECT_PLAN_SCHEMA (in module sollertia_forgery.orchestration.planning)

project_root (sollertia_forgery.orchestration.GenericPendingJob attribute) ProjectManifest (class in sollertia_forgery.managing) pull() (sollertia_forgery.server.Server method) PUPIL_AREA_PX2 (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) PUPIL_CENTER_X_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) PUPIL_CENTER_Y_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) PUPIL_DIAMETER_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) PUPIL_FIT_CONDITION (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) PUPIL_FIT_RESIDUAL_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) PUPIL_IN_EYE_X (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) PUPIL_IN_EYE_Y (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) PUPIL_REFLECTION_OFFSET_X_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) PUPIL_REFLECTION_OFFSET_Y_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) PupilColumn (class in sollertia_forgery.mesoscope_vr.video_tracking) push() (sollertia_forgery.server.Server method)

Q

queued (sollertia_forgery.orchestration.SchedulerReading attribute)

R

read_batch_outcome() (in module sollertia_forgery.orchestration) read_ledger() (in module sollertia_forgery.orchestration) read_prepared_batch() (in module sollertia_forgery.orchestration) read_prepared_batches() (in module sollertia_forgery.orchestration) read_rows() (sollertia_forgery.orchestration.ExecutionHost method) (sollertia_forgery.orchestration.LocalHost static method) (sollertia_forgery.orchestration.RemoteHost method) read_scheduler_records() (in module sollertia_forgery.orchestration) reconcile_local_jobs() (in module sollertia_forgery.orchestration) reconcile_remote_jobs() (in module sollertia_forgery.orchestration) record_prepared_batch() (in module sollertia_forgery.orchestration) reference_samples (sollertia_forgery.shared_assets.AssemblyGeometry attribute) REFLECTION_X_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) REFLECTION_Y_PX (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.video_tracking.PupilColumn attribute) REGISTER (sollertia_forgery.two_photon.SingleRecordingJobNames attribute) REINFORCING_GUIDED (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) remediation (sollertia_forgery.orchestration.AllocationResolution attribute) remote_batch_directory() (in module sollertia_forgery.orchestration) REMOTE_HOST_LABEL (in module sollertia_forgery.orchestration.reconcile) REMOTE_JOB_WALLTIME_MINUTES (in module sollertia_forgery.orchestration.remote) remote_script_path (sollertia_forgery.server.Job attribute) remote_state_directory() (in module sollertia_forgery.server) remote_state_path() (in module sollertia_forgery.server) RemoteHost (class in sollertia_forgery.orchestration) remove() (sollertia_forgery.server.Server method) RENAME_JOB_NAME (in module sollertia_forgery.video.pipeline) render_allocation() (in module sollertia_forgery.orchestration) RESERVED_CORES (in module sollertia_forgery.orchestration.local) reset_jobs() (sollertia_forgery.orchestration.ExecutionHost method) (sollertia_forgery.orchestration.LocalHost static method) (sollertia_forgery.orchestration.RemoteHost method) RESET_REMEDIATION (in module sollertia_forgery.orchestration.remote) reset_stranded_jobs() (in module sollertia_forgery.orchestration) reset_tracked_jobs() (in module sollertia_forgery.orchestration) resolve_allocations() (in module sollertia_forgery.orchestration) resolve_assembly_geometry_resolver() (in module sollertia_forgery.registries) resolve_assembly_source_resolver() (in module sollertia_forgery.registries) resolve_batch() (sollertia_forgery.orchestration.SubmissionLedger method) resolve_batch_host() (in module sollertia_forgery.orchestration) resolve_batches() (in module sollertia_forgery.orchestration) resolve_camera_video() (in module sollertia_forgery.video) resolve_concurrency_limits() (in module sollertia_forgery.orchestration) resolve_concurrency_reservations() (in module sollertia_forgery.orchestration) resolve_core_allocations() (in module sollertia_forgery.orchestration) resolve_dataset_plan() (in module sollertia_forgery.orchestration)

resolve_eligible_microcontroller_modules() (in module sollertia_forgery.registries) resolve_forging_admission_pipelines() (in module sollertia_forgery.registries) resolve_forging_assembly_worker() (in module sollertia_forgery.registries) resolve_forging_column_descriptions() (in module sollertia_forgery.registries) resolve_host_memory_mb() (in module sollertia_forgery.orchestration) resolve_job_cores() (in module sollertia_forgery.orchestration) resolve_live_allocations() (in module sollertia_forgery.orchestration) resolve_mesoscope_assembly_geometry() (in module sollertia_forgery.mesoscope_vr) resolve_mesoscope_assembly_sources() (in module sollertia_forgery.mesoscope_vr) resolve_microcontroller_event_codes() (in module sollertia_forgery.registries) resolve_microcontroller_parsers() (in module sollertia_forgery.registries) resolve_multi_recording_configuration() (in module sollertia_forgery.mesoscope_vr) resolve_multi_recording_configuration_resolver() (in module sollertia_forgery.registries) resolve_multi_recording_session_types() (in module sollertia_forgery.registries) resolve_openmp_runtime() (in module sollertia_forgery.shared_assets) resolve_pose_prediction_locator() (in module sollertia_forgery.registries) resolve_project_root() (in module sollertia_forgery.orchestration) resolve_queried_allocations() (in module sollertia_forgery.orchestration) resolve_runtime_binding() (in module sollertia_forgery.registries) resolve_session_plan() (in module sollertia_forgery.orchestration) resolve_session_tracker_path() (in module sollertia_forgery.shared_assets) resolve_single_recording_configuration() (in module sollertia_forgery.mesoscope_vr) resolve_single_recording_configuration_resolver() (in module sollertia_forgery.registries) resolve_state() (sollertia_forgery.orchestration.SchedulerReading method) resolve_status() (sollertia_forgery.orchestration.SchedulerReading method) resolve_tracker_claims() (in module sollertia_forgery.orchestration) resolve_tracker_paths() (sollertia_forgery.orchestration.ExecutionHost method) (sollertia_forgery.orchestration.LocalHost static method) (sollertia_forgery.orchestration.RemoteHost static method) resolve_two_photon_data_locator() (in module sollertia_forgery.registries) resolve_video_tracking() (in module sollertia_forgery.registries) REVOKED (sollertia_forgery.server.JobStatus attribute) REWARD (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) root (sollertia_forgery.server.Server property) (sollertia_forgery.server.ServerConfiguration attribute) run_batch_job() (in module sollertia_forgery.orchestration) run_checksum_processing_pipeline() (in module sollertia_forgery.managing) run_forging_pipeline() (in module sollertia_forgery.forging) run_microcontroller_processing_pipeline() (in module sollertia_forgery.microcontrollers) run_runtime_processing_pipeline() (in module sollertia_forgery.runtime) run_two_photon_processing_pipeline() (in module sollertia_forgery.two_photon) run_video_processing_pipeline() (in module sollertia_forgery.video) RUNNING (sollertia_forgery.server.JobStatus attribute) RUNNING_ALLOCATION (in module sollertia_forgery.orchestration.remote) RUNTIME (sollertia_forgery.shared_assets.ProcessingPipelines attribute) RUNTIME_JOB_NAME (in module sollertia_forgery.runtime.pipeline) runtime_job_prerequisites() (in module sollertia_forgery.runtime) RUNTIME_SOURCE_ID (in module sollertia_forgery.mesoscope_vr.runtime) RUNTIME_STATE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute)

S

scheduler_state (sollertia_forgery.orchestration.AllocationResolution attribute) SchedulerReading (class in sollertia_forgery.orchestration) SCREENS (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) Server (class in sollertia_forgery.server) server (sollertia_forgery.orchestration.RemoteHost property) ServerConfiguration (class in sollertia_forgery.server) SESSION_PIPELINES (in module sollertia_forgery.shared_assets.pipelines) SESSION_UNIT (in module sollertia_forgery.orchestration.dispatch) SETTLED_ALLOCATION (in module sollertia_forgery.orchestration.remote) SINGLE_DAY_CELL_FLUORESCENCE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) SINGLE_DAY_NEUROPIL_FLUORESCENCE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) SINGLE_DAY_SPIKES (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) SINGLE_DAY_SUBTRACTED_FLUORESCENCE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) SingleRecordingJobNames (class in sollertia_forgery.two_photon) slf-checksum command line option --no-progress --regenerate-checksum --session-path --workers -np -rc -sp -w slf-clean command line option --pipeline --unit-path -p -up slf-dataset-state command line option --dataset-path -dp slf-forge command line option --dataset-name --force-recreate --job-id --no-progress --project-path --recreate-animal --session --workers -dn -f -id -np -pp -ra -s -w slf-manifest command line option --project-path -pp slf-manifest-create command line option --no-progress -np slf-manifest-print command line option --animal --notes --summary -a -n -s slf-mcp command line option --transport -t slf-omp command line option --force --source --target --yes -f -s -t -y slf-plan-dataset command line option --dataset-path --regenerate-plan -dp -rp slf-plan-project command line option --project-path -pp slf-plan-session command line option --regenerate-plan --session-path -rp -sp slf-process command line option --job-id --no-progress --session-path --workers -id -np -sp -w slf-process-two-photon command line option --binarize --combine --process --register --target-plane -b -cb -p -r -tp

slf-process-video command line option --energy --target-camera --timestamp --track -en -tc -tr -ts slf-reset command line option --job-id --pipeline --unit-path -id -p -up slf-server-batches command line option --allocations --batch-id -a -b slf-server-configure command line option --environment --host --password --root --username -e -h -p -r -u slf-server-discover command line option --project -p slf-server-print command line option --end-time --job-data --job-id --queue --start-time --user -et -id -j -q -st -u slf-server-pull command line option --destination --remote-path -d -r slf-server-retire-batch command line option --batch-id --drop-without-outcome --force -b -do -f sollertia_forgery.forging module sollertia_forgery.managing module sollertia_forgery.mesoscope_vr module sollertia_forgery.microcontrollers module sollertia_forgery.orchestration module sollertia_forgery.registries module sollertia_forgery.runtime module sollertia_forgery.server module sollertia_forgery.shared_assets module sollertia_forgery.two_photon module sollertia_forgery.video module source_samples (sollertia_forgery.shared_assets.AssemblyGeometry attribute) specifier (sollertia_forgery.orchestration.GenericPendingJob attribute) SPEED_CM_S (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) STALLED_BATCH (in module sollertia_forgery.orchestration.remote) status (sollertia_forgery.orchestration.GenericPendingJob attribute) statuses (sollertia_forgery.orchestration.SchedulerReading attribute) STRANDED_ALLOCATION (in module sollertia_forgery.orchestration.remote) submission (sollertia_forgery.orchestration.AllocationResolution attribute) SubmissionBatch (class in sollertia_forgery.orchestration) SubmissionLedger (class in sollertia_forgery.orchestration) submissions (sollertia_forgery.orchestration.SubmissionBatch attribute) submit_batch() (in module sollertia_forgery.orchestration) submit_job() (sollertia_forgery.server.Server method) submitted_at (sollertia_forgery.orchestration.SubmissionBatch attribute) succeeded_job_keys (sollertia_forgery.orchestration.JobExecutionState attribute) summarize() (sollertia_forgery.managing.ProjectManifest method) sync_project_state() (in module sollertia_forgery.orchestration) SYSTEM_STATE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute)

T

TERMINAL_JOB_STATUSES (in module sollertia_forgery.server.server) thread_ceiling (sollertia_forgery.orchestration.JobExecutionState attribute) TIME_US (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) TIMEOUT (sollertia_forgery.server.JobStatus attribute) TORQUE_N_CM (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute)

tracker (sollertia_forgery.orchestration.AllocationResolution attribute) TRACKING_JOB_NAME (in module sollertia_forgery.video.pipeline) TRIAL (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) TRIAL_TYPE (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute) TWO_PHOTON (sollertia_forgery.shared_assets.ProcessingPipelines attribute) two_photon_job_prerequisites() (in module sollertia_forgery.two_photon)

U

UNKNOWN (sollertia_forgery.server.JobStatus attribute) unreadable_reason (sollertia_forgery.orchestration.SchedulerReading attribute) UNRESOLVED (sollertia_forgery.server.JobStatus attribute) (sollertia_forgery.shared_assets.OpenMPStatus attribute)

user (sollertia_forgery.server.Server property) username (sollertia_forgery.server.ServerConfiguration attribute)

V

verdict (sollertia_forgery.orchestration.AllocationResolution attribute) verify_openmp_runtime() (in module sollertia_forgery.shared_assets)

VIDEO (sollertia_forgery.shared_assets.ProcessingPipelines attribute) video_job_prerequisites() (in module sollertia_forgery.video)

W

walltime_minutes (sollertia_forgery.orchestration.SubmissionBatch attribute) WATER_UL (sollertia_forgery.mesoscope_vr.DatasetColumn attribute) (sollertia_forgery.mesoscope_vr.metadata.DatasetColumn attribute)

worker (sollertia_forgery.orchestration.JobExecutionState attribute)