allensdk.internal.brain_observatory package

Subpackages

• allensdk.internal.brain_observatory.resources package
  • Module contents
• allensdk.internal.brain_observatory.util package
  • Submodules
    • allensdk.internal.brain_observatory.util.multi_session_utils module
  • 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
    • EyeCalibration.compute_area()
    • EyeCalibration.cr_position_in_mouse_eye_coordinates()
    • EyeCalibration.pupil_position_in_mouse_eye_coordinates()
    • EyeCalibration.pupil_position_on_monitor_in_cm()
    • EyeCalibration.pupil_position_on_monitor_in_degrees()
  • base_object_to_eye_rotation_matrix()
  • object_norm_eye_coordinates()
  • object_rotation_matrix()
  • project_to_plane()
• allensdk.internal.brain_observatory.fit_ellipse module
  • FitEllipse
    • FitEllipse.choose_inliers()
    • FitEllipse.fit_ellipse()
    • FitEllipse.outlier_cost()
    • FitEllipse.ransac_fit()
  • 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
    • CvInputStream.close()
    • CvInputStream.open()
  • FfmpegInputStream
    • FfmpegInputStream.close()
    • FfmpegInputStream.create_images()
    • FfmpegInputStream.open()
  • FfmpegOutputStream
    • FfmpegOutputStream.close()
    • FfmpegOutputStream.open()
  • FrameInputStream
    • FrameInputStream.close()
    • FrameInputStream.create_images()
    • FrameInputStream.open()
  • FrameOutputStream
    • FrameOutputStream.close()
    • FrameOutputStream.open()
    • FrameOutputStream.write()
  • 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
    • MaskSet.close()
    • MaskSet.close_sets()
    • MaskSet.count
    • MaskSet.detect_duplicates()
    • MaskSet.detect_unions()
    • MaskSet.distance()
    • MaskSet.intersection()
    • MaskSet.intersection_size()
    • MaskSet.mask()
    • MaskSet.mask_is_union_of_set()
    • MaskSet.overlap_fraction()
    • MaskSet.size()
    • MaskSet.union()
    • MaskSet.union_size()
  • 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
    • TrainingLabelClassifier.decision_function()
  • TrainingMultiLabelClassifier
    • TrainingMultiLabelClassifier.get_eXcluded()
    • TrainingMultiLabelClassifier.label_data()
  • 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
    • OphysTimeAligner.behavior_video_timestamps
    • OphysTimeAligner.clipped_stim_timestamps
    • OphysTimeAligner.corrected_behavior_video_timestamps
    • OphysTimeAligner.corrected_eye_video_timestamps
    • OphysTimeAligner.corrected_ophys_timestamps
    • OphysTimeAligner.corrected_stim_timestamps
    • OphysTimeAligner.dataset
    • OphysTimeAligner.eye_video_timestamps
    • OphysTimeAligner.monitor_delay
    • OphysTimeAligner.ophys_timestamps
    • OphysTimeAligner.stim_timestamps
  • 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