{ "extractor": "human-explainers.h5_extract.calibration_snapshot.v1", "h5py_version": "3.16.0", "source_file": "/home/jeremy/orange_data/exp/unsorted/2026_08_25_23_12_06/citrus/citsess_45fac0f71f098cf00f44065893c773b7847ab224edba618cb2a1c9744731065e_redbat.h5", "source_sha256": "2e01101135134d264fc495579a0bac0873f6118fd842a69a02141cdd6ab70be2", "source_bytes": 89467969, "root_attrs": { "active_ipc_source": "SHAMAN", "arena_id": "arena_1", "artifact_schema_id": "behavior_v1", "behavior_mode": "free", "canvas_name": "shadow", "display_mode_height_reported_px": 1080, "display_mode_observation_source": "xrandr_selected_output_verbose_current_mode", "display_mode_pixel_clock_reported_mhz": 296.7, "display_mode_width_reported_px": 1920, "display_refresh_rate_reported_hz": 119.88, "display_refresh_rate_source": "xrandr_selected_output_current_mode", "display_submission_rate_source": "citrus_frame_rate_limiter_nominal", "display_submission_rate_target_hz": 120.0, "display_swap_interval": 0, "expected_bounding_boxes_rows": 173563, "expected_chaser_states_rows": 180232, "expected_display_frame_submission_rows": 215977, "expected_events_rows": 152, "expected_frame_metadata_rows": 216232, "expected_independent_motion_grid_states_rows": 0, "expected_moving_grating_states_rows": 0, "expected_runtime_trials_rows": 4, "experimental_chamber": "palm1", "hostname": "pancake0.hhmi.org", "ipc_first_nonzero_frame_id": 1008, "ipc_first_nonzero_frame_timestamp_ns_session": 1388876200, "ipc_reader_init_status": "initialized", "ipc_source_name": "/shm_cam_2010093", "loaded_protocol_filepath": "redbat.json", "protocol_name_from_definition": "redbat", "recording_subtype": "free", "recording_type": "behavior", "rig_id": "omnifin0", "session_output_dir": "/home/jeremy/orange_data/exp/unsorted/2026_08_25_23_12_06/citrus", "session_start_iso8601_utc": "2026-08-26T03-12-19Z", "session_start_ns_epoch": 1787713939114183878, "session_status": "COMPLETE", "session_uuid": "citsess_45fac0f71f098cf00f44065893c773b7847ab224edba618cb2a1c9744731065e", "software_version": "", "stimulus_frame_rate_nominal_hz": 120.0, "stimulus_output_height": 1080, "stimulus_output_width": 1920, "tracking_bounding_boxes_rows": 173563, "tracking_chaser_states_rows": 180232 }, "calibration_snapshot": { "attrs": { "projection_geometry_authority_canvas_name": "shadow", "projection_geometry_authority_mode": "local_canvas", "selected_canvas_name": "shadow" }, "groups": { "2010093": { "attrs": { "camera_view_down_in_canvas_angle_deg": -90.35123443603516, "camera_view_down_in_canvas_x": -0.006130152847617865, "camera_view_down_in_canvas_y": -0.999981164932251, "camera_view_right_in_canvas_angle_deg": -0.35421979427337646, "camera_view_right_in_canvas_x": 0.9999808073043823, "camera_view_right_in_canvas_y": -0.0061822617426514626, "direction_mapping_canvas_angle_convention": "0=right,90=down", "direction_mapping_handedness": "mirrored", "direction_mapping_ref_camera_x": 2229.577392578125, "direction_mapping_ref_camera_y": 2245.14892578125, "direction_mapping_ref_canvas_x": 259.0, "direction_mapping_ref_canvas_y": 332.0, "direction_mapping_scale_x": 0.07898100465536118, "direction_mapping_scale_y": 0.07965237647294998, "pixels_per_mm_camera": 52.75507354736328, "pixels_per_mm_projector": 4.184098243713379, "real_world_ref_mm": 5.0 }, "groups": { "scale_models": { "attrs": { "scale_model_count": 1, "schema_id": "citrus.plane_scale_models_snapshot", "schema_version": 1 }, "groups": { "projected_surface": { "attrs": { "clicked_point1_x_camera_px": -1.0, "clicked_point1_y_camera_px": -1.0, "clicked_point2_x_camera_px": -1.0, "clicked_point2_y_camera_px": -1.0, "kind": "projective_local_jacobian_at_target_origin", "notes": "Loaded from immutable active projected-surface scale pointer", "pixels_per_mm_camera": 52.75507354736328, "pixels_per_mm_projector": 4.184098243713379, "real_world_ref_mm": 5.0, "scale_image_path": "/home/jeremy/orange_data/calibrations/sessions/calsess_2026_08_10T01_53_54Z_shadow/artifacts/Cam2010093_arena_1/scale_observations/calgrp_2026_08_10T01_53_53Z_shadow_projected_surface_scale_calibration_projected_surface_g1/observation.json", "status": "accepted", "target_plane": "projected_surface" }, "datasets": { "scale_image_png_buffer": { "attrs": {}, "dtype": "uint8", "shape": [ 63028 ], "omitted": { "bytes": 63028, "sha256": "41995b7a900c35691bac273a6950075435ce990bca7403dbbfbe2c131530a9d9" } } } } } } }, "datasets": { "homography_image_png_buffer": { "attrs": {}, "dtype": "uint8", "shape": [ 8034245 ], "omitted": { "bytes": 8034245, "sha256": "977804b4ccf5003e71c244eff67a3296d853b7abdaa5feec364bdd38ab5f575b" } }, "homography_matrix": { "attrs": { "arena_config_name": "arena_1", "axes": "x_right_y_down", "camera_id": "2010093", "canvas_name": "shadow", "coordinate_origin": "top_left", "dest_frame": "final_display_canvas_px", "homography_artifact_checksum_algorithm": "fnv1a64", "homography_artifact_checksum_fnv1a64": "af351bdb2310837d", "homography_artifact_exists": "true", "homography_artifact_filename": "homography_arena_1_2010093.yml", "homography_artifact_mtime_unix_ns": 1786323758019198158, "homography_artifact_path": "/home/jeremy/citrus/targets/rigs/omnifin0/shadow/calibration_artifacts/homography_arena_1_2010093.yml", "homography_artifact_size_bytes": 1295, "homography_fit_inlier_count": 81, "homography_fit_max_reprojection_error_px": 0.2432277899465086, "homography_fit_point_count": 81, "homography_fit_quality_available": "true", "homography_fit_quality_schema": "citrus.homography_fit_quality.v1", "homography_fit_rms_reprojection_error_px": 0.12110689401871437, "homography_payload_source": "runtime_arena_config.homography_matrix", "homography_provenance_schema": "citrus.homography_provenance.v1", "image_space": "raw", "rig_id": "omnifin0", "runtime_matrix_checksum_algorithm": "sha256", "runtime_matrix_checksum_serialization": "json_row_major_float64_v1", "runtime_matrix_checksum_sha256": "sha256:cfdbbbf45b75226f42cdadeb77831a9cd5fa7b7d31834237f41e18d85c729112", "source_frame": "camera_view_px" }, "dtype": "float64", "shape": [ 3, 3 ], "value": [ [ 0.07874250445494245, -0.0005856985662148073, 84.33456319725997 ], [ -0.0006186948810984491, -0.07962950658326917, 511.62381365417457 ], [ -3.960271677654378e-07, -3.2541264852901244e-07, 1.0 ] ] }, "homography_matrix_yml": { "attrs": { "arena_config_name": "arena_1", "axes": "x_right_y_down", "camera_id": "2010093", "canvas_name": "shadow", "coordinate_origin": "top_left", "dest_frame": "final_display_canvas_px", "homography_artifact_checksum_algorithm": "fnv1a64", "homography_artifact_checksum_fnv1a64": "af351bdb2310837d", "homography_artifact_exists": "true", "homography_artifact_filename": "homography_arena_1_2010093.yml", "homography_artifact_mtime_unix_ns": 1786323758019198158, "homography_artifact_path": "/home/jeremy/citrus/targets/rigs/omnifin0/shadow/calibration_artifacts/homography_arena_1_2010093.yml", "homography_artifact_size_bytes": 1295, "homography_fit_inlier_count": 81, "homography_fit_max_reprojection_error_px": 0.2432277899465086, "homography_fit_point_count": 81, "homography_fit_quality_available": "true", "homography_fit_quality_schema": "citrus.homography_fit_quality.v1", "homography_fit_rms_reprojection_error_px": 0.12110689401871437, "homography_payload_source": "resolved_calibration_artifact_file", "homography_provenance_schema": "citrus.homography_provenance.v1", "image_space": "raw", "rig_id": "omnifin0", "serialization_format": "opencv_yml", "source_frame": "camera_view_px" }, "dtype": "object", "shape": [], "value": "%YAML:1.0\n---\nartifact_schema_id: \"citrus.calibration.homography_candidate\"\nartifact_schema_version: 1\ncandidate_id: homography_arena_1_2010093_holder_operational_calgrp_2026_08_10T00_54_10Z_shadow_homography_grid_projected_surface_g4\ncandidate_set_id: homography_set_holder_operational_calgrp_2026_08_10T00_54_10Z_shadow_homography_grid_projected_surface_g4\nhomography_direction: camera_native_px_to_final_display_canvas_px\ntarget_plane: projected_surface\npattern_mode: circular_rings\norientation_validation_status: passed\norientation_normalization_transform: \"\"\nconfiguration_fingerprint: \"sha256:d7c8768401b5e6756f0eb839c8c496723fcac64d1649ae407ad0e77f42fd90e6\"\nsource_capture_checksum: \"fnv1a64:8c6521cd3dd7b4ff\"\nfit_quality_schema: \"citrus.homography_fit_quality.v2\"\npoint_count: 81\ninlier_count: 81\nrms_reprojection_error_px: 0.12110689401871437\nmax_reprojection_error_px: 0.24322778994650859\nholdout_rms_reprojection_error_px: 0.13175429435202413\nholdout_max_reprojection_error_px: 0.22372118118053888\nhomography_matrix: !!opencv-matrix\n rows: 3\n cols: 3\n dt: d\n data: [ 0.07874250445494245, -0.0005856985662148073,\n 84.334563197259968, -0.00061869488109844912,\n -0.079629506583269172, 511.62381365417457,\n -3.9602716776543781e-07, -3.2541264852901244e-07, 1. ]\n" }, "scale_image_png_buffer": { "attrs": {}, "dtype": "uint8", "shape": [ 63028 ], "omitted": { "bytes": 63028, "sha256": "41995b7a900c35691bac273a6950075435ce990bca7403dbbfbe2c131530a9d9" } } } }, "arena_geometry": { "attrs": { "arena_geometry_source": "active_camera_calibration", "arena_origin_in_canvas_x_px": 90.0, "arena_origin_in_canvas_y_px": 164.0, "arena_region_center_in_canvas_x_px": 264.0, "arena_region_center_in_canvas_y_px": 338.0, "arena_region_height_px": 348.0, "arena_region_width_px": 348.0, "coordinate_frame": "arena_relative_canvas_px", "coordinate_origin": "top_left_of_active_arena", "experimental_area_center_x_px": 173.0, "experimental_area_center_y_px": 173.0, "experimental_area_corner_radius_mm": 11.99231243133545, "experimental_area_corner_radius_px": 50.1770133972168, "experimental_area_height_mm": 80.0, "experimental_area_height_px": 334.72784423828125, "experimental_area_radius_mm": 40.0, "experimental_area_radius_px": 167.36392211914062, "experimental_area_shape": "CIRCLE", "experimental_area_width_mm": 80.0, "experimental_area_width_px": 334.72784423828125, "x_axis_direction": "right", "y_axis_direction": "down" } }, "calibration_pattern": { "attrs": { "coordinate_frame": "arena_relative_canvas_px", "dot_radius_px": 5.0, "grid_cols": 10, "grid_rows": 10, "mask_policy": "experimental_area", "mask_policy_note": "full_arena_unmasked bypasses experimental-area masking for broad calibration; experimental_area applies the runtime area mask", "pattern_mode": "circular_rings", "ring_chirality_marker_radius_scale": 1.2999999523162842, "ring_count": 4, "ring_dots_inner": 8, "ring_dots_outer": 32, "ring_include_center_dot": 1, "ring_inner_radius_px": 40.0, "ring_orientation_marker_angle_deg": 0.0, "ring_orientation_marker_radius_scale": 1.600000023841858, "ring_outer_radius_px": 140.0, "ring_show_chirality_marker": 0, "ring_show_orientation_marker": 1, "schema_id": "citrus.calibration_pattern_snapshot", "schema_version": 1, "verification_include_center_dot": 1, "verification_inner_angle_offset_deg": 45.0, "verification_inner_point_count": 4, "verification_inner_radius_fraction": 0.3799999952316284, "verification_outer_angle_offset_deg": 22.5, "verification_outer_point_count": 8, "verification_outer_radius_fraction": 0.7799999713897705 } }, "tank": { "attrs": { "source_dish_id": "18973_1", "tank_design_file_exists": "true", "tank_design_file_path": "/home/jeremy/citrus/targets/tank_designs/palm1.json", "tank_design_id": "palm1", "tank_design_json_checksum_algorithm": "fnv1a64", "tank_design_json_checksum_fnv1a64": "bdc4027069fca70b", "tank_design_json_source": "resolved_tank_design_file", "tank_design_spec_filename": "palm1.json", "tank_geometry_schema": "citrus.tank_design_spec.v1", "tank_placement_schema": "citrus.tank_placement.v1" }, "datasets": { "tank_design_json": { "attrs": { "payload_source": "resolved_tank_design_file", "schema_id": "citrus.tank_design_spec" }, "dtype": "object", "shape": [], "value": "{\n \"$schema\": \"../../src/schemas/tank_design_spec.schema.json\",\n \"biological_plane_assumptions\": {\n \"assumed_larvae_eye_height_mm\": 8.0,\n \"estimated_fish_plane\": \"operator_estimated\",\n \"nominal_water_depth_mm\": 5.0\n },\n \"derived_optics\": {\n \"total_acrylic_mm\": 7.760000228881836,\n \"water_path_mm\": 8.0,\n \"z_eff_formula\": \"water_path + (n_water / n_acrylic) * total_acrylic\",\n \"z_eff_mm\": 14.94233512878418\n },\n \"description\": \"Thin bottomed tank design by Sam Goetsch\",\n \"dimensions\": {\n \"bottom_thickness_mm\": 3.0,\n \"inner_diameter_mm\": 80.0,\n \"outer_diameter_mm\": 90.0,\n \"usable_area_diameter_mm\": 80.0,\n \"wall_height_mm\": 3.0,\n \"wall_thickness_mm\": 5.0\n },\n \"display_name\": \"palm1\",\n \"legacy_dish_model_type\": \"CUSTOM\",\n \"materials\": {\n \"shelf_material\": \"acrylic\",\n \"shelf_refractive_index\": 1.4900000095367432,\n \"tank_material\": \"acrylic\",\n \"tank_refractive_index\": 1.4900000095367432,\n \"water_refractive_index\": 1.3329999446868896\n },\n \"projection_stack\": {\n \"bath_water_gap_mm\": 0.0,\n \"diffuser_sandwich_mm\": 0.0,\n \"projector_shelf_thickness_mm\": 4.760000228881836\n },\n \"schema_id\": \"citrus.tank_design_spec\",\n \"schema_version\": 1,\n \"shape\": \"circular\",\n \"source\": {\n \"kind\": \"citrus_in_app_creator\",\n \"notes\": \"Created in Citrus UI; verify physical measurements before treating as authoritative.\",\n \"path\": \"targets/tank_designs/palm1.json\"\n },\n \"tank_design_id\": \"palm1\"\n}\n" }, "tank_placement_json": { "attrs": { "payload_source": "arena_config_snapshot", "schema_id": "citrus.tank_placement" }, "dtype": "object", "shape": [], "value": "{\n \"arena_config_name\": \"arena_1\",\n \"camera_id\": \"2010093\",\n \"placement_source\": \"arena_config_active_camera_calibration\",\n \"schema_id\": \"citrus.tank_placement\",\n \"schema_version\": 1,\n \"source_dish_id\": \"18973_1\",\n \"tank_design_id\": \"palm1\",\n \"tank_design_spec_filename\": \"palm1.json\"\n}" } } } }, "datasets": { "arena_config_json": { "attrs": {}, "dtype": "object", "shape": [], "value": "{\n \"active_camera_id\": \"2010093\",\n \"arena_region_height_mm\": 83.46649169921875,\n \"arena_region_width_mm\": 83.46649169921875,\n \"calculated_z_eff_mm\": 14.94233512878418,\n \"calibration_pattern_mask_policy\": \"experimental_area\",\n \"calibration_pattern_mode\": \"circular_rings\",\n \"calibration_ring_chirality_marker_radius_scale\": 1.2999999523162842,\n \"calibration_ring_count\": 4,\n \"calibration_ring_dots_inner\": 8,\n \"calibration_ring_dots_outer\": 32,\n \"calibration_ring_include_center_dot\": true,\n \"calibration_ring_inner_radius_px\": 40.0,\n \"calibration_ring_orientation_marker_angle_deg\": 0.0,\n \"calibration_ring_orientation_marker_radius_scale\": 1.600000023841858,\n \"calibration_ring_outer_radius_px\": 140.0,\n \"calibration_ring_show_chirality_marker\": false,\n \"calibration_ring_show_orientation_marker\": true,\n \"calibration_verification_include_center_dot\": true,\n \"calibration_verification_inner_angle_offset_deg\": 45.0,\n \"calibration_verification_inner_point_count\": 4,\n \"calibration_verification_inner_radius_fraction\": 0.3799999952316284,\n \"calibration_verification_outer_angle_offset_deg\": 22.5,\n \"calibration_verification_outer_point_count\": 8,\n \"calibration_verification_outer_radius_fraction\": 0.7799999713897705,\n \"camera_calibrations\": [\n {\n \"arena_center_x_px\": 259,\n \"arena_center_y_px\": 332,\n \"arena_height_px\": 348,\n \"arena_width_px\": 348,\n \"camera_id\": \"2010093\",\n \"homography_detector_strategy\": \"\",\n \"homography_fit_inlier_count\": 0,\n \"homography_fit_max_reprojection_error_px\": 0.0,\n \"homography_fit_method\": \"\",\n \"homography_fit_point_count\": 0,\n \"homography_fit_quality_available\": false,\n \"homography_fit_rms_reprojection_error_px\": 0.0,\n \"homography_image_path\": \"Cam2010093_arena1_homography.png\",\n \"native_height_px\": 4512,\n \"native_width_px\": 4512,\n \"pixels_per_mm_camera\": 52.75507354736328,\n \"pixels_per_mm_projector\": 4.184098243713379,\n \"real_world_ref_mm\": 5.0,\n \"scale_image_path\": \"/home/jeremy/orange_data/calibrations/sessions/calsess_2026_08_10T01_53_54Z_shadow/artifacts/Cam2010093_arena_1/scale_observations/calgrp_2026_08_10T01_53_53Z_shadow_projected_surface_scale_calibration_projected_surface_g1/observation.json\",\n \"scale_models\": [\n {\n \"clicked_points_camera_px\": [\n {\n \"x\": -1.0,\n \"y\": -1.0\n },\n {\n \"x\": -1.0,\n \"y\": -1.0\n }\n ],\n \"kind\": \"projective_local_jacobian_at_target_origin\",\n \"notes\": \"Loaded from immutable active projected-surface scale pointer\",\n \"pixels_per_mm_camera\": 52.75507354736328,\n \"pixels_per_mm_projector\": 4.184098243713379,\n \"real_world_ref_mm\": 5.0,\n \"scale_image_path\": \"/home/jeremy/orange_data/calibrations/sessions/calsess_2026_08_10T01_53_54Z_shadow/artifacts/Cam2010093_arena_1/scale_observations/calgrp_2026_08_10T01_53_53Z_shadow_projected_surface_scale_calibration_projected_surface_g1/observation.json\",\n \"status\": \"accepted\",\n \"target_plane\": \"projected_surface\"\n }\n ]\n }\n ],\n \"config_name\": \"arena_1\",\n \"dish_config\": {\n \"biological\": {\n \"adult_eye_height_mm\": 8.0,\n \"larvae_eye_height_mm\": 8.0,\n \"media_type\": \"E3 embryo medium\",\n \"water_fill_depth_mm\": 5.0\n },\n \"dimensions\": {\n \"diameter_mm\": 80.0,\n \"diffuser_sandwich_mm\": 0.0,\n \"dish_base_thickness_mm\": 3.0,\n \"projector_base_thickness_mm\": 4.760000228881836,\n \"wall_height_mm\": 3.0\n },\n \"dish_name\": \"palm1\",\n \"dish_shape\": \"circular\",\n \"dish_type\": 3,\n \"materials\": {\n \"air_refractive_index\": 1.0,\n \"base_material\": 1,\n \"base_refractive_index\": 1.4900000095367432,\n \"diffuser_type\": \"Paper diffuser\",\n \"dish_material\": 1,\n \"dish_refractive_index\": 1.4900000095367432,\n \"water_refractive_index\": 1.3329999446868896\n },\n \"optics\": {\n \"calculated_with_params_hash\": 0.0,\n \"compression_start_radius_mm\": 16.94875144958496,\n \"snell_window_radius_mm\": 16.94875144958496,\n \"z_eff_adult_mm\": 14.94233512878418,\n \"z_eff_current_mm\": 14.94233512878418,\n \"z_eff_larvae_mm\": 14.94233512878418\n }\n },\n \"dish_shape\": \"circular\",\n \"dot_radius_px\": 5.0,\n \"experimental_area_center_x_px\": 173.0,\n \"experimental_area_center_y_px\": 173.0,\n \"experimental_area_corner_radius_mm\": 11.99231243133545,\n \"experimental_area_corner_radius_px\": 50.1770133972168,\n \"experimental_area_height_mm\": 80.0,\n \"experimental_area_height_px\": 334.72784423828125,\n \"experimental_area_radius_mm\": 40.0,\n \"experimental_area_radius_px\": 167.36392211914063,\n \"experimental_area_shape\": \"CIRCLE\",\n \"experimental_area_width_mm\": 80.0,\n \"experimental_area_width_px\": 334.72784423828125,\n \"experimental_chamber\": \"palm1\",\n \"grid_cols\": 10,\n \"grid_rows\": 10,\n \"ipc_frame_trigger_count\": 60,\n \"ipc_source_name\": \"/shm_cam_2010093\",\n \"ipc_source_type\": \"SHAMAN\",\n \"ipc_start_trigger\": \"ON_IPC_FRAME_COUNT\",\n \"selected_dish_type\": 2,\n \"selected_dish_type_name\": \"palm1\",\n \"shaman_v2_live_state_enabled\": false,\n \"shaman_v2_source_name\": \"\",\n \"tank_design_id\": \"palm1\",\n \"tank_design_spec_filename\": \"palm1.json\"\n}" } } } }