allensdk.brain_observatory.stimulus_info module¶
- class allensdk.brain_observatory.stimulus_info.BinaryIntervalSearchTree(search_list)[source]¶
Bases:
object
- class allensdk.brain_observatory.stimulus_info.BrainObservatoryMonitor(experiment_geometry=None)[source]¶
Bases:
Monitor
http://help.brain-map.org/display/observatory/Documentation?preview=/10616846/10813485/VisualCoding_VisualStimuli.pdf # noqa: E501 https://www.cnet.com/products/asus-pa248q/specs/
- class allensdk.brain_observatory.stimulus_info.ExperimentGeometry(distance, mon_height_cm, mon_width_cm, mon_res, eyepoint)[source]¶
Bases:
object
- property warp_coordinates¶
- class allensdk.brain_observatory.stimulus_info.Monitor(n_pixels_r, n_pixels_c, panel_size, spatial_unit)[source]¶
Bases:
object
- property aspect_ratio¶
- grating_to_screen(phase, spatial_frequency, orientation, distance_from_monitor, p2p_amp=256, baseline=127, translation=(0, 0))[source]¶
- property height¶
- lsn_image_to_screen(img, stimulus_type, origin='lower', background_color=127, translation=(0, 0))[source]¶
- property mask¶
- property panel_size¶
- property pixel_size¶
- property width¶
- allensdk.brain_observatory.stimulus_info.all_stimuli()[source]¶
Return a list of all stimuli in the data set
- allensdk.brain_observatory.stimulus_info.get_spatial_grating(height=None, aspect_ratio=None, ori=None, pix_per_cycle=None, phase=None, p2p_amp=2, baseline=0)[source]¶
- allensdk.brain_observatory.stimulus_info.get_spatio_temporal_grating(t, temporal_frequency=None, **kwargs)[source]¶
- allensdk.brain_observatory.stimulus_info.lsn_coordinate_to_monitor_coordinate(lsn_coordinate, monitor_shape, stimulus_type)[source]¶
- allensdk.brain_observatory.stimulus_info.make_display_mask(display_shape=(1920, 1200))[source]¶
Build a display-shaped mask that indicates which pixels are on screen after warping the stimulus.
- allensdk.brain_observatory.stimulus_info.map_monitor_coordinate_to_stimulus_coordinate(monitor_coordinate, monitor_shape, stimulus_type)[source]¶
- allensdk.brain_observatory.stimulus_info.map_monitor_coordinate_to_template_coordinate(monitor_coord, monitor_shape, template_shape)[source]¶
- allensdk.brain_observatory.stimulus_info.map_stimulus(source_stimulus_coordinate, source_stimulus_type, target_stimulus_type, monitor_shape)[source]¶
- allensdk.brain_observatory.stimulus_info.map_stimulus_coordinate_to_monitor_coordinate(template_coordinate, monitor_shape, stimulus_type)[source]¶
- allensdk.brain_observatory.stimulus_info.map_template_coordinate_to_monitor_coordinate(template_coord, monitor_shape, template_shape)[source]¶
- allensdk.brain_observatory.stimulus_info.mask_stimulus_template(template_display_coords, template_shape, display_mask=None, threshold=1.0)[source]¶
Build a mask for a stimulus template of a given shape and display coordinates that indicates which part of the template is on screen after warping.
- Parameters:
- template_display_coords: list
list of (x,y) display coordinates
- template_shape: tuple
(width,height) of the display template
- display_mask: np.ndarray
boolean 2D mask indicating which display coordinates are on screen after warping.
- threshold: float
Fraction of pixels associated with a template display coordinate that should remain on screen to count as belonging to the mask.
- Returns:
- tuple: (template mask, pixel fraction)
- allensdk.brain_observatory.stimulus_info.monitor_coordinate_to_lsn_coordinate(monitor_coordinate, monitor_shape, stimulus_type)[source]¶
- allensdk.brain_observatory.stimulus_info.monitor_coordinate_to_natural_movie_coordinate(monitor_coordinate, monitor_shape)[source]¶
- allensdk.brain_observatory.stimulus_info.natural_movie_coordinate_to_monitor_coordinate(natural_movie_coordinate, monitor_shape)[source]¶
- allensdk.brain_observatory.stimulus_info.natural_scene_coordinate_to_monitor_coordinate(natural_scene_coordinate, monitor_shape)[source]¶
- allensdk.brain_observatory.stimulus_info.sessions_with_stimulus(stimulus)[source]¶
Return the names of the sessions that contain a given stimulus.
- allensdk.brain_observatory.stimulus_info.stimuli_in_session(session, allow_unknown=True)[source]¶
Return a list what stimuli are available in a given session.
- Parameters:
- session: string
- Must be one of: [
stimulus_info.THREE_SESSION_A, stimulus_info.THREE_SESSION_B, stimulus_info.THREE_SESSION_C, stimulus_info.THREE_SESSION_C2 ]
- allensdk.brain_observatory.stimulus_info.warp_stimulus_coords(vertices, distance=15.0, mon_height_cm=32.5, mon_width_cm=51.0, mon_res=(1920, 1200), eyepoint=(0.5, 0.5))[source]¶
For a list of screen vertices, provides a corresponding list of texture coordinates.
- Parameters:
- vertices: numpy.ndarray
[[x0,y0], [x1,y1], …] A set of vertices to convert to texture positions.
- distance: float
distance from the monitor in cm.
- mon_height_cm: float
monitor height in cm
- mon_width_cm: float
monitor width in cm
- mon_res: tuple
monitor resolution (x,y)
- eyepoint: tuple
- Returns:
- np.ndarray
x,y coordinates shaped like the input that describe what pixel coordinates are displayed an the input coordinates after warping the stimulus.