allensdk.internal package

Subpackages

• allensdk.internal.api package
  • Subpackages
    • allensdk.internal.api.queries package
      • Submodules
      • Module contents
  • Submodules
    • allensdk.internal.api.api_prerelease module
      • ApiPrerelease
    • allensdk.internal.api.lims_api module
      • LimsApi
    • allensdk.internal.api.mtrain_api module
  • Module contents
    • OneOrMoreResultExpectedError
    • PostgresQueryMixin
      • PostgresQueryMixin.fetchall()
      • PostgresQueryMixin.fetchone()
      • PostgresQueryMixin.get_connection()
      • PostgresQueryMixin.get_cursor()
      • PostgresQueryMixin.select()
      • PostgresQueryMixin.select_one()
    • db_connection_creator()
    • psycopg2_select()
• allensdk.internal.brain_observatory package
  • Subpackages
    • allensdk.internal.brain_observatory.resources package
      • Module contents
    • allensdk.internal.brain_observatory.util package
      • Submodules
      • Module contents
  • Submodules
    • allensdk.internal.brain_observatory.annotated_region_metrics module
      • create_region_mask()
      • eccentricity()
      • get_metrics()
      • retinotopy_metric()
    • allensdk.internal.brain_observatory.demix_report module
      • background_trace()
      • compute_correlations()
      • compute_correlations_without_masks()
      • compute_non_overlap_masks()
      • compute_non_overlap_traces()
      • correlation_report()
      • plot_masks()
    • allensdk.internal.brain_observatory.demixer module
      • demix_time_dep_masks()
      • find_negative_baselines()
      • find_negative_transients_threshold()
      • find_zero_baselines()
      • identify_valid_masks()
      • plot_negative_baselines()
      • plot_negative_transients()
      • plot_overlap_masks_lengthOne()
      • plot_traces()
      • plot_transients()
      • rolling_window()
    • allensdk.internal.brain_observatory.eye_calibration module
      • EyeCalibration
      • base_object_to_eye_rotation_matrix()
      • object_norm_eye_coordinates()
      • object_rotation_matrix()
      • project_to_plane()
    • allensdk.internal.brain_observatory.fit_ellipse module
      • FitEllipse
      • ellipse_angle_of_rotation()
      • ellipse_angle_of_rotation2()
      • ellipse_axis_length()
      • ellipse_center()
      • fit_ellipse()
      • rotate_vector()
      • test_fit()
    • allensdk.internal.brain_observatory.frame_stream module
      • CvInputStream
      • FfmpegInputStream
      • FfmpegOutputStream
      • FrameInputStream
      • FrameOutputStream
      • ImageOutputStream
    • allensdk.internal.brain_observatory.itracker module
    • allensdk.internal.brain_observatory.itracker_utils module
      • default_ray()
      • eccentricity()
      • filter_bad_params()
      • generate_rays()
      • initial_cr_point()
      • initial_pupil_point()
      • medfilt_custom()
      • median_absolute_deviation()
      • post_process_cr()
      • post_process_pupil()
      • rotate_ray()
      • sobel_grad()
    • allensdk.internal.brain_observatory.mask_set module
      • MaskSet
      • bb_dist()
      • make_bbs()
    • allensdk.internal.brain_observatory.mouse module
    • allensdk.internal.brain_observatory.ophys_session_decomposition module
      • export_frame_to_hdf5()
      • load_frame()
      • open_view_on_binary()
      • read_strided()
    • allensdk.internal.brain_observatory.roi_filter module
    • allensdk.internal.brain_observatory.roi_filter_utils module
      • CRITERIA()
      • TrainingLabelClassifier
      • TrainingMultiLabelClassifier
      • calculate_max_border()
      • get_indices_by_distance()
      • get_rois()
      • order_rois_by_object_list()
    • allensdk.internal.brain_observatory.run_itracker module
    • allensdk.internal.brain_observatory.time_sync module
      • OphysTimeAligner
      • calculate_monitor_delay()
      • corrected_video_timestamps()
      • get_alignment_array()
      • get_keys()
      • get_ophys_data_length()
      • get_photodiode_events()
      • get_real_photodiode_events()
      • get_stim_data_length()
      • get_video_length()
  • Module contents
• allensdk.internal.core package
  • Submodules
    • allensdk.internal.core.lims_pipeline_module module
      • PipelineModule
      • default_argument_parser()
      • run_module()
    • allensdk.internal.core.lims_utilities module
      • append_well_known_file()
      • connect()
      • convert_from_titan_linux()
      • get_input_json()
      • get_well_known_file_by_name()
      • get_well_known_file_by_type()
      • get_well_known_files_by_name()
      • get_well_known_files_by_type()
      • linux_to_windows()
      • query()
      • safe_system_path()
      • select()
    • allensdk.internal.core.mouse_connectivity_cache_prerelease module
      • MouseConnectivityCachePrerelease
    • allensdk.internal.core.simpletree module
      • SimpleTree
    • allensdk.internal.core.swc module
      • Marker
      • read_marker_file()
      • read_swc()
  • Module contents
• allensdk.internal.ephys package
  • Submodules
    • allensdk.internal.ephys.core_feature_extract module
      • extract_data()
      • filter_sweeps()
      • filtered_sweep_numbers()
      • find_coarse_long_square_amp_delta()
      • find_stim_start()
      • find_sweep_stim_start()
      • generate_output_cell_features()
      • nan_get()
      • save_qc_figures()
      • update_output_sweep_features()
    • allensdk.internal.ephys.plot_qc_figures module
      • exp_curve()
      • get_features()
      • get_spikes()
      • get_time_string()
      • load_experiment()
      • main()
      • make_cell_html()
      • make_cell_page()
      • make_sweep_html()
      • make_sweep_page()
      • mask_nulls()
      • plot_cell_figures()
      • plot_fi_curve_figures()
      • plot_hero_figures()
      • plot_images()
      • plot_instantaneous_threshold_thumbnail()
      • plot_long_square_summary()
      • plot_ramp_figures()
      • plot_rheo_figures()
      • plot_sag_figures()
      • plot_short_square_figures()
      • plot_single_ap_values()
      • plot_subthreshold_long_square_figures()
      • plot_sweep_figures()
      • plot_sweep_set_summary()
      • plot_sweep_value_figures()
      • save_figure()
    • allensdk.internal.ephys.plot_qc_figures3 module
      • exp_curve()
      • get_features()
      • get_spikes()
      • get_time_string()
      • load_experiment()
      • make_cell_html()
      • make_cell_page()
      • make_sweep_html()
      • make_sweep_page()
      • mask_nulls()
      • plot_cell_figures()
      • plot_fi_curve_figures()
      • plot_hero_figures()
      • plot_images()
      • plot_instantaneous_threshold_thumbnail()
      • plot_long_square_summary()
      • plot_ramp_figures()
      • plot_rheo_figures()
      • plot_sag_figures()
      • plot_short_square_figures()
      • plot_single_ap_values()
      • plot_subthreshold_long_square_figures()
      • plot_sweep_figures()
      • plot_sweep_set_summary()
      • plot_sweep_value_figures()
      • save_figure()
  • Module contents
• allensdk.internal.model package
  • Subpackages
    • allensdk.internal.model.biophysical package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.internal.model.glif package
      • Submodules
      • Module contents
  • Submodules
    • allensdk.internal.model.AIC module
      • AIC()
      • AICc()
      • BIC()
    • allensdk.internal.model.GLM module
      • create_basis_IPSP()
      • ff()
      • invnl()
      • makeBasis_StimKernel()
      • makeBasis_StimKernel_exp()
      • makeFitStruct_GLM()
      • nlin()
      • normalizecols()
      • sameconv()
    • allensdk.internal.model.data_access module
      • load_sweep()
      • load_sweeps()
      • subsample_data()
  • Module contents
• allensdk.internal.morphology package
  • Submodules
    • allensdk.internal.morphology.compartment module
      • Compartment
    • allensdk.internal.morphology.morphology module
      • Morphology
    • allensdk.internal.morphology.morphvis module
      • MorphologyColors
      • calculate_scale()
      • create_image()
      • draw_density_hist()
      • draw_morphology()
    • allensdk.internal.morphology.node module
      • Node
      • euclidean_distance()
      • midpoint()
    • allensdk.internal.morphology.validate_swc module
      • TestNode
      • main()
      • resave_swc()
      • validate_swc()
  • Module contents
• allensdk.internal.mouse_connectivity package
  • Subpackages
    • allensdk.internal.mouse_connectivity.interval_unionize package
      • Submodules
      • Module contents
    • allensdk.internal.mouse_connectivity.projection_thumbnail package
      • Submodules
      • Module contents
    • allensdk.internal.mouse_connectivity.tissuecyte_stitching package
      • Submodules
      • Module contents
  • Module contents
• allensdk.internal.notebooks package
  • Submodules
    • allensdk.internal.notebooks.execute_notebooks module
  • Module contents
• allensdk.internal.pipeline_modules package
  • Subpackages
    • allensdk.internal.pipeline_modules.gbm package
      • Submodules
      • Module contents
  • Submodules
    • allensdk.internal.pipeline_modules.run_annotated_region_metrics module
      • debug()
      • load_arrays()
      • main()
    • allensdk.internal.pipeline_modules.run_demixing module
      • assert_exists()
      • debug()
      • get_path()
      • main()
      • parse_input()
    • allensdk.internal.pipeline_modules.run_dff_computation module
      • main()
      • parse_input()
    • allensdk.internal.pipeline_modules.run_eye_tracking module
    • allensdk.internal.pipeline_modules.run_neuropil_correction module
      • adjust_r_for_negativity()
      • debug()
      • debug_plot()
      • main()
    • allensdk.internal.pipeline_modules.run_observatory_analysis module
      • debug()
      • get_experiment_nwb_file()
      • get_experiment_session()
      • main()
    • allensdk.internal.pipeline_modules.run_observatory_container_thumbnails module
    • allensdk.internal.pipeline_modules.run_observatory_thumbnails module
      • build_cell_plots()
      • build_correlation_plots()
      • build_drifting_gratings()
      • build_experiment_thumbnails()
      • build_eye_tracking_plots()
      • build_locally_sparse_noise()
      • build_natural_movie()
      • build_natural_scenes()
      • build_plots()
      • build_receptive_field()
      • build_speed_tuning()
      • build_static_gratings()
      • build_type()
      • debug()
      • get_experiment_analysis_file()
      • get_experiment_files()
      • get_experiment_nwb_file()
      • get_input_data()
      • lsna_check_hvas()
      • main()
      • parse_input()
    • allensdk.internal.pipeline_modules.run_ophys_eye_calibration module
      • debug()
      • get_wkf()
      • main()
      • parse_input_data()
      • write_output()
    • allensdk.internal.pipeline_modules.run_ophys_session_decomposition module
      • convert_frame()
      • create_fake_metadata()
      • debug()
      • main()
      • parse_input()
    • allensdk.internal.pipeline_modules.run_ophys_time_sync module
      • TimeSyncOutputs
      • TimeSyncWriter
      • check_stimulus_delay()
      • main()
      • run_ophys_time_sync()
    • allensdk.internal.pipeline_modules.run_roi_filter module
    • allensdk.internal.pipeline_modules.run_tissuecyte_projection_thumbnail_from_json module
    • allensdk.internal.pipeline_modules.run_tissuecyte_stitching_classic module
    • allensdk.internal.pipeline_modules.run_tissuecyte_unionize_cav_from_json module
    • allensdk.internal.pipeline_modules.run_tissuecyte_unionize_classic_counts_from_json module
    • allensdk.internal.pipeline_modules.run_tissuecyte_unionize_classic_from_json module
      • main()
  • Module contents

Module contents