class CircularTarget(object):
def __init__(self,
target_radius=2,
target_color=(1, 0, 0, .5),
starting_pos=np.zeros(3)):
self.target_color = target_color
self.default_target_color = tuple(self.target_color)
self.target_radius = target_radius
self.target_color = target_color
self.position = starting_pos
self.int_position = starting_pos
self._pickle_init()
def _pickle_init(self):
self.sphere = Sphere(radius=self.target_radius,
color=self.target_color)
self.graphics_models = [self.sphere]
self.sphere.translate(*self.position)
def move_to_position(self, new_pos):
self.int_position = new_pos
self.drive_to_new_pos()
def drive_to_new_pos(self):
raise NotImplementedError
def __init__(self, *args, **kwargs):
super(TargetCapture, self).__init__(*args, **kwargs)
self.origin_target = Sphere(radius=self.origin_size,
color=(1, 0, 0, .5))
self.add_model(self.origin_target)
self.cursor = Sphere(radius=self.cursor_radius, color=(.5, 0, .5, 1))
self.add_model(self.cursor)
def _pickle_init(self):
super(VirtualKinChainWithToolLink, self)._pickle_init()
self.tool_tip_cursor = Sphere(radius=self.link_radii[-1] / 2,
color=RED)
self.tool_base_cursor = Sphere(radius=self.link_radii[-1] / 2,
color=BLUE)
self.graphics_models = [
self.link_groups[0], self.tool_tip_cursor, self.tool_base_cursor
]
def __init__(self, *args, **kwargs):
# Add the target and cursor locations to the task data to be saved to
# file
self.dtype = [('target', 'f', (3, )), ('cursor', 'f', (3, ))]
super(ManualControl, self).__init__(*args, **kwargs)
self.terminus_target = Sphere(radius=self.terminus_size,
color=(1, 0, 0, .5))
self.add_model(self.terminus_target)
# Initialize target location variables
self.location = np.array([0, 0, 0])
self.target_xz = np.array([0, 0])
def __init__(self, *args, **kwargs):
super(TentacleMultiConfigObstacleAvoidance,
self).__init__(*args, **kwargs)
## Create an obstacle object, hidden by default
self.obstacle = Sphere(radius=self.obstacle_radius + 0.6,
color=(0, 0, 1, .5))
self.obstacle_on = False
self.obstacle_pos = np.ones(3) * np.nan
self.hit_obstacle = False
self.add_model(self.obstacle)
def __init__(self, *args, **kwargs):
# Add the target and cursor locations to the task data to be saved to
# file
super(TestGraphics, self).__init__(*args, **kwargs)
self.dtype = [('target', 'f', (3,)), ('cursor', 'f', (3,)), (('target_index', 'i', (1,)))]
self.target1 = Sphere(radius=self.target_radius, color=(1,0,0,.5))
self.add_model(self.target1)
self.target2 = Sphere(radius=self.target_radius, color=(1,0,0,.5))
self.add_model(self.target2)
# Initialize target location variable
self.target_location = np.array([0,0,0])
class TestGraphics(Sequence, Window):
status = dict(wait=dict(stop=None), )
#initial state
state = "wait"
target_radius = 2.
#create targets, cursor objects, initialize
def __init__(self, *args, **kwargs):
# Add the target and cursor locations to the task data to be saved to
# file
#super(TestGraphics, self).__init__(*args, **kwargs)
super().__init__(*args, **kwargs)
self.dtype = [('target', 'f', (3, )), ('cursor', 'f', (3, )),
(('target_index', 'i', (1, )))]
self.target1 = Sphere(radius=self.target_radius, color=(1, 0, 0, .5))
self.add_model(self.target1)
self.target2 = Sphere(radius=self.target_radius, color=(1, 0, 0, 0.5))
self.add_model(self.target2)
# Initialize target location variable
self.target_location = np.array([0.0, 0.0, 0.0])
##### HELPER AND UPDATE FUNCTIONS ####
#<<<<<<< HEAD
def _get_renderer(self):
return stereo.MirrorDisplay(self.window_size, self.fov, 1, 1024,
self.screen_dist, self.iod)
def _cycle(self):
super()._cycle()
#### STATE FUNCTIONS ####
def _while_wait(self):
#print("_while_wait")
delta_movement = np.array([0, 0, 0.01])
self.target_location += delta_movement
self.target1.translate(self.target_location[0],
self.target_location[1],
self.target_location[2],
reset=True)
self.requeue()
self.draw_world()
print('current target 1 position ' +
np.array2string(self.target_location))
class BMIControlManipulatedFB(bmimultitasks.BMIControlMulti):
feedback_rate = traits.Float(60, desc="Rate in hz that cursor position is updated on screen (best if factor of 60)")
task_update_rate = traits.Float(60, desc="Rate in hz that decoded cursor position is updated within task (best if factor of 60)")
ordered_traits = ['session_length', 'assist_level', 'assist_time', 'feedback_rate', 'task_update_rate']
def __init__(self, *args, **kwargs):
super(BMIControlManipulatedFB, self).__init__(*args, **kwargs)
self.visible_cursor = Sphere(radius=self.cursor_radius, color=(1,1,1,1))
self.add_model(self.visible_cursor)
self.cursor_visible = True
def init(self):
self.dtype.append(('visible_cursor','f8',3))
super(BMIControlManipulatedFB, self).init()
self.feedback_num = int(60.0/self.feedback_rate)
self.task_update_num = int(60.0/self.task_update_rate)
self.loopcount = 0
def update_cursor(self):
''' Update the cursor's location and visibility status.'''
pt = self.get_cursor_location()
prev = self.cursor_visible
self.cursor_visible = False
if prev != self.cursor_visible:
self.show_object(self.cursor, show=False) #self.cursor.detach()
self.requeue()
#update the "real" cursor location only according to specified task update rate
if self.loopcount%self.task_update_num==0:
if pt is not None:
self.move_cursor(pt)
#update the visible cursor location only according to specified feedback rate
if self.loopcount%self.feedback_num==0:
loc = self.cursor.xfm.move
self.visible_cursor.translate(*loc,reset=True)
def _cycle(self):
''' Overwriting parent methods since this one works differently'''
self.update_assist_level()
self.task_data['assist_level'] = self.current_assist_level
self.update_cursor()
self.task_data['cursor'] = self.cursor.xfm.move.copy()
self.task_data['target'] = self.target_location.copy()
self.task_data['target_index'] = self.target_index
self.task_data['visible_cursor'] = self.visible_cursor.xfm.move.copy()
self.loopcount += 1
#write to screen
self.draw_world()
def __init__(self, *args, **kwargs):
super(ApproachAvoidanceTask, self).__init__(*args, **kwargs)
self.cursor_visible = True
# Add graphics models for the plant and targets to the window
self.plant = plantlist[self.plant_type]
self.plant_vis_prev = True
# Add graphics models for the plant and targets to the window
if hasattr(self.plant, 'graphics_models'):
for model in self.plant.graphics_models:
self.add_model(model)
self.current_pt=np.zeros([3]) #keep track of current pt
self.last_pt=np.zeros([3]) #kee
## Declare cursor
#self.dtype.append(('cursor', 'f8', (3,)))
if 0: #hasattr(self.arm, 'endpt_cursor'):
self.cursor = self.arm.endpt_cursor
else:
self.cursor = Sphere(radius=self.cursor_radius, color=self.cursor_color)
self.add_model(self.cursor)
self.cursor.translate(*self.get_arm_endpoint(), reset=True)
## Instantiate the targets. Target 1 is center target, Target H is target with high probability of reward, Target L is target with low probability of reward.
self.target1 = Sphere(radius=self.target_radius, color=self.target_color) # center target
self.add_model(self.target1)
self.targetR = Sphere(radius=self.target_radius, color=self.target_color) # left target
self.add_model(self.targetH)
self.targetL = Sphere(radius=self.target_radius, color=self.target_color) # right target
self.add_model(self.targetL)
###STOPPED HERE: should define Rect target here and then adapt length during task. Also,
### be sure to change all targetH instantiations to targetR.
# Initialize target location variable.
self.target_location1 = np.array([0,0,0])
self.target_locationR = np.array([-self.starting_dist,0,0])
self.target_locationL = np.array([self.starting_dist,0,0])
self.target1.translate(*self.target_location1, reset=True)
self.targetH.translate(*self.target_locationR, reset=True)
self.targetL.translate(*self.target_locationL, reset=True)
# Initialize colors for high probability and low probability target. Color will not change.
self.targetH.color = self.color_targets*self.color1 + (1 - self.color_targets)*self.color2 # high is magenta if color_targets = 1, juicyorange otherwise
self.targetL.color = (1 - self.color_targets)*self.color1 + self.color_targets*self.color2
#set target colors
self.target1.color = (1,0,0,.5) # center target red
# Initialize target location variable
self.target_location = np.array([0, 0, 0])
# Declare any plant attributes which must be saved to the HDF file at the _cycle rate
for attr in self.plant.hdf_attrs:
self.add_dtype(*attr)
def __init__(self, *args, **kwargs):
if SIM:
self.rx_port = ('localhost', 60000)
self.tx_port = ('localhost', 60001)
else:
self.rx_port = ('10.0.0.1', 60000)
self.tx_port = ('10.0.0.14', 60001)
self.has_force_sensor = kwargs.pop('has_force_sensor', True)
self.hdf_attrs = [('joint_angles', 'f8', (5,)), ('joint_velocities', 'f8', (5,)), ('joint_applied_torque', 'f8', (5,)),]
if self.has_force_sensor and not ('endpt_force' in self.hdf_attrs):
self.hdf_attrs.append(('endpt_force', 'f8', (1,)))
# Initialize sockets for transmitting velocity commands / receiving sensor data
tx_sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
self.tx_sock = tx_sock
## kinematic chain
self.kin_chain = ActiveExoChain()
# joint limits in radians, based on mechanical limits---some configurations
# may still be outside the comfortable range for the subject
self.kin_chain.joint_limits = [(-1.25, 1.25), (0, 1.7), (-0.95, 0.9), (0, 1.4), (-1.5, 1.5)]
## Graphics, for experimenter only
self.link_lengths = link_lengths
self.cursor = Sphere(radius=arm_radius/2, color=arm_color)
self.upperarm_graphics = Cylinder(radius=arm_radius, height=self.link_lengths[0], color=arm_color)
# self.upperarm_graphics.xfm.translate(*exo_chain_graphics_base_loc)
self.forearm_graphics = Cone(radius1=arm_radius, radius2=arm_radius/3, height=self.link_lengths[1], color=arm_color)
self.forearm_graphics.xfm.translate(*exo_chain_graphics_base_loc)
self.graphics_models = [self.upperarm_graphics, self.forearm_graphics, self.cursor]
self.enabled = True
super(ActiveExoPlant, self).__init__(*args, **kwargs)
class VirtualKinChainWithToolLink(RobotArmGen2D):
def _pickle_init(self):
super(VirtualKinChainWithToolLink, self)._pickle_init()
self.tool_tip_cursor = Sphere(radius=self.link_radii[-1] / 2,
color=RED)
self.tool_base_cursor = Sphere(radius=self.link_radii[-1] / 2,
color=BLUE)
self.graphics_models = [
self.link_groups[0], self.tool_tip_cursor, self.tool_base_cursor
]
def _update_link_graphics(self):
super(VirtualKinChainWithToolLink, self)._update_link_graphics()
joint_angles = self.calc_joint_angles()
spatial_joint_pos = self.kin_chain.spatial_positions_of_joints(
joint_angles)
self.tool_tip_cursor.translate(*spatial_joint_pos[:, -1], reset=True)
self.tool_base_cursor.translate(*spatial_joint_pos[:, -2], reset=True)
def __init__(self, *args, **kwargs):
super(ArmPlant, self).__init__(*args, **kwargs)
self.cursor_visible = True
# Initialize the arm
self.arm = ik.test_3d
self.arm_vis_prev = True
if self.arm_class == 'CursorPlant':
pass
else:
self.dtype.append(('joint_angles', 'f8', (self.arm.num_joints, )))
self.dtype.append(('arm_visible', 'f8', (1, )))
self.add_model(self.arm)
## Declare cursor
self.dtype.append(('cursor', 'f8', (3, )))
self.cursor = Sphere(radius=self.cursor_radius,
color=self.cursor_color)
self.add_model(self.cursor)
self.cursor.translate(*self.arm.get_endpoint_pos(), reset=True)
def __init__(self, *args, **kwargs):
super(BMIControlManipulatedFB, self).__init__(*args, **kwargs)
self.visible_cursor = Sphere(radius=self.cursor_radius, color=(1,1,1,1))
self.add_model(self.visible_cursor)
self.cursor_visible = True
class MovementTraining(Window):
status = dict(wait=dict(stop=None, move_start="movement"),
movement=dict(move_end="reward", move_stop="wait",
stop=None),
reward=dict(reward_end="wait"))
log_exclude = set((("wait", "move_start"), ("movement", "move_stop")))
#initial state
state = "wait"
path = [[0, 0, 0]]
speed = 0
frame_offset = 2
over = 0
inside = 0
#settable traits
movement_distance = traits.Float(
1, desc="Minimum movement distance to trigger reward")
speed_range = traits.Tuple(
20, 30, desc="Range of movement speed in cm/s to trigger reward")
reward_time = traits.Float(14)
#initialize
def __init__(self, **kwargs):
super(MovementTraining, self).__init__(**kwargs)
self.cursor = Sphere(radius=.5, color=(.5, 0, .5, 1))
self.add_model(self.cursor)
def update_cursor(self):
#get data from 13th marker on motion tracker- take average of all data points since last poll
pt = self.motiondata.get()
if len(pt) > 0:
pt = pt[:, 14, :]
# NOTE!!! The marker on the hand was changed from #0 to #14 on
# 5/19/13 after LED #0 broke. All data files saved before this date
# have LED #0 controlling the cursor.
pt = pt[~np.isnan(pt).any(1)]
if len(pt) > 0:
pt = pt.mean(0)
self.path.append(pt)
#ignore y direction
t = pt * .25
t[1] = 0
#move cursor to marker location
self.cursor.translate(*t[:3], reset=True)
else:
self.path.append(self.path[-1])
if len(self.path) > self.frame_offset:
self.path.pop(0)
d = np.sqrt((self.path[-1][0] - self.path[0][0])**2 +
(self.path[-1][1] - self.path[0][1])**2 +
(self.path[-1][2] - self.path[0][2])**2)
self.speed = d / (self.frame_offset / 60)
if self.speed > self.speed_range[0]:
self.over += 1
if self.speed_range[0] < self.speed < self.speed_range[1]:
self.inside += 1
#write to screen
self.draw_world()
def _start_wait(self):
self.over = 0
self.inside = 0
def _while_wait(self):
self.update_cursor()
def _while_movement(self):
self.update_cursor()
def _while_reward(self):
self.update_cursor()
def _test_move_start(self, ts):
return self.over > self.frame_offset
def _test_move_end(self, ts):
return ts > self.movement_distance / self.speed_range[0]
def _test_move_stop(self, ts):
return self.inside > self.frame_offset
def _test_reward_end(self, ts):
return ts > self.reward_time
class ArmPlant(Window):
'''
This task creates a RobotArm object and allows it to move around the screen based on either joint or endpoint
positions. There is a spherical cursor at the end of the arm. The links of the arm can be visible or hidden.
'''
background = (0, 0, 0, 1)
arm_visible = traits.Bool(
True,
desc='Specifies whether entire arm is displayed or just endpoint')
cursor_radius = traits.Float(.5, desc="Radius of cursor")
cursor_color = (.5, 0, .5, 1)
arm_class = traits.OptionsList(*plantlist,
bmi3d_input_options=plantlist.keys())
starting_pos = (5, 0, 5)
def __init__(self, *args, **kwargs):
super(ArmPlant, self).__init__(*args, **kwargs)
self.cursor_visible = True
# Initialize the arm
self.arm = ik.test_3d
self.arm_vis_prev = True
if self.arm_class == 'CursorPlant':
pass
else:
self.dtype.append(('joint_angles', 'f8', (self.arm.num_joints, )))
self.dtype.append(('arm_visible', 'f8', (1, )))
self.add_model(self.arm)
## Declare cursor
self.dtype.append(('cursor', 'f8', (3, )))
self.cursor = Sphere(radius=self.cursor_radius,
color=self.cursor_color)
self.add_model(self.cursor)
self.cursor.translate(*self.arm.get_endpoint_pos(), reset=True)
def _cycle(self):
'''
Calls any update functions necessary and redraws screen. Runs 60x per second by default.
'''
## Run graphics commands to show/hide the arm if the visibility has changed
if self.arm_class != 'CursorPlant':
if self.arm_visible != self.arm_vis_prev:
self.arm_vis_prev = self.arm_visible
self.show_object(self.arm, show=self.arm_visible)
self.move_arm()
self.update_cursor()
if self.cursor_visible:
self.task_data['cursor'] = self.cursor.xfm.move.copy()
else:
#if the cursor is not visible, write NaNs into cursor location saved in file
self.task_data['cursor'] = np.array([np.nan, np.nan, np.nan])
if self.arm_class != 'CursorPlant':
if self.arm_visible:
self.task_data['arm_visible'] = 1
else:
self.task_data['arm_visible'] = 0
super(ArmPlant, self)._cycle()
## Functions to move the cursor using keyboard/mouse input
def get_mouse_events(self):
import pygame
events = []
for btn in pygame.event.get(
(pygame.MOUSEBUTTONDOWN, pygame.MOUSEBUTTONUP)):
events = events + [btn.button]
return events
def get_key_events(self):
import pygame
return pygame.key.get_pressed()
def move_arm(self):
'''
allows use of keyboard keys to test movement of arm. Use QW/OP for joint movements, arrow keys for endpoint movements
'''
import pygame
keys = self.get_key_events()
joint_speed = (np.pi / 6) / 60
hand_speed = .2
x, y, z = self.arm.get_endpoint_pos()
if keys[pygame.K_RIGHT]:
x = x - hand_speed
self.arm.set_endpoint_pos(np.array([x, 0, z]))
if keys[pygame.K_LEFT]:
x = x + hand_speed
self.arm.set_endpoint_pos(np.array([x, 0, z]))
if keys[pygame.K_DOWN]:
z = z - hand_speed
self.arm.set_endpoint_pos(np.array([x, 0, z]))
if keys[pygame.K_UP]:
z = z + hand_speed
self.arm.set_endpoint_pos(np.array([x, 0, z]))
if self.arm.num_joints == 2:
xz, xy = self.get_arm_joints()
e = np.array([xz[0], xy[0]])
s = np.array([xz[1], xy[1]])
if keys[pygame.K_q]:
s = s - joint_speed
self.set_arm_joints([e[0], s[0]], [e[1], s[1]])
if keys[pygame.K_w]:
s = s + joint_speed
self.set_arm_joints([e[0], s[0]], [e[1], s[1]])
if keys[pygame.K_o]:
e = e - joint_speed
self.set_arm_joints([e[0], s[0]], [e[1], s[1]])
if keys[pygame.K_p]:
e = e + joint_speed
self.set_arm_joints([e[0], s[0]], [e[1], s[1]])
if self.arm.num_joints == 4:
jts = self.get_arm_joints()
keyspressed = [
keys[pygame.K_q], keys[pygame.K_w], keys[pygame.K_e],
keys[pygame.K_r]
]
for i in range(self.arm.num_joints):
if keyspressed[i]:
jts[i] = jts[i] + joint_speed
self.set_arm_joints(jts)
def get_cursor_location(self):
return self.arm.get_endpoint_pos()
def set_arm_endpoint(self, pt, **kwargs):
self.arm.set_endpoint_pos(pt, **kwargs)
def set_arm_joints(self, angle_xz, angle_xy):
self.arm.set_intrinsic_coordinates(angle_xz, angle_xy)
def get_arm_joints(self):
return self.arm.get_intrinsic_coordinates()
def update_cursor(self):
'''
Update the cursor's location and visibility status.
'''
pt = self.get_cursor_location()
if pt is not None:
self.move_cursor(pt)
def move_cursor(self, pt):
''' Move the cursor object to the specified 3D location. '''
if not hasattr(self.arm, 'endpt_cursor'):
self.cursor.translate(*pt[:3], reset=True)
class TargetCapture(Sequence, FixationTraining):
status = dict(wait=dict(start_trial="origin", stop=None),
origin=dict(enter_target="origin_hold", stop=None),
origin_hold=dict(leave_early="hold_penalty", hold="reward"),
reward=dict(reward_end="target_change"),
hold_penalty=dict(penalty_end="pre_target_change"),
pre_target_change=dict(tried_enough='target_change',
not_tried_enough='wait'),
target_change=dict(target_change_end='wait'))
#create settable traits
origin_size = traits.Float(1, desc="Radius of origin targets"
) #add error if target is smaller than cursor
origin_hold_time = traits.Float(2,
desc="Length of hold required at origin")
hold_penalty_time = traits.Float(
3, desc="Length of penalty time for target hold error")
exit_radius = 1.5 #Multiplier for the actual radius which is considered 'exiting' the target
no_data_count = 0
tries = 0
scale_factor = 3.5 #scale factor for converting hand movement to screen movement (1cm hand movement = 3.5cm cursor movement)
cursor_radius = .5
def __init__(self, *args, **kwargs):
super(TargetCapture, self).__init__(*args, **kwargs)
self.origin_target = Sphere(radius=self.origin_size,
color=(1, 0, 0, .5))
self.add_model(self.origin_target)
self.cursor = Sphere(radius=self.cursor_radius, color=(.5, 0, .5, 1))
self.add_model(self.cursor)
def _start_wait(self):
super(TargetCapture, self)._start_wait()
#set target color
self.origin_target.color = (1, 0, 0, .5)
#hide target from previous trial
self.show_origin(False)
def show_origin(self, show=False):
if show:
self.origin_target.attach()
else:
self.origin_target.detach()
self.requeue()
def _start_origin(self):
if self.tries == 0:
#retrieve location of next origin target
o = self.next_trial.T[0]
#move target to correct location
self.origin_target.translate(*o, reset=True)
#make visible
self.show_origin(True)
def _end_origin_hold(self):
#change target color
self.origin_target.color = (0, 1, 0, 0.5)
def _start_hold_penalty(self):
self.tries += 1
#hide target
self.show_origin(False)
def _start_target_change(self):
self.tries = 0
def _test_target_change_end(self, ts):
return True
def _test_enter_target(self, ts):
#get the current cursor location and target location, return true if center of cursor is inside target (has to be close enough to center to be fully inside)
c = self.cursor.xfm.move
t = self.origin_target.xfm.move
d = np.sqrt((c[0] - t[0])**2 + (c[1] - t[1])**2 + (c[2] - t[2])**2)
return d <= self.origin_target.radius - self.cursor.radius
def _test_leave_early(self, ts):
c = self.cursor.xfm.move
t = self.origin_target.xfm.move
d = np.sqrt((c[0] - t[0])**2 + (c[1] - t[1])**2 + (c[2] - t[2])**2)
rad = self.origin_target.radius - self.cursor.radius
return d > rad * self.exit_radius
def _test_hold(self, ts):
return ts >= self.origin_hold_time
def _test_penalty_end(self, ts):
if self.state == "fixation_penalty":
return ts > self.fixation_penalty_time
else:
return ts > self.hold_penalty_time
def _test_tried_enough(self, ts):
return self.tries == 3
def _test_not_tried_enough(self, ts):
return self.tries != 3
def _update(self, pt):
if len(pt) > 0:
self.cursor.translate(*pt[:3], reset=True)
#if no data has come in for at least 3 frames, hide cursor
elif self.no_data_count > 2:
self.no_data_count += 1
self.cursor.detach()
self.requeue()
else:
self.no_data_count += 1
def update_cursor(self):
#get data from 1st marker on motion tracker- take average of all data points since last poll
pt = self.motiondata.get()
if len(pt) > 0:
pt = pt[:, 14, :]
# NOTE!!! The marker on the hand was changed from #0 to #14 on
# 5/19/13 after LED #0 broke. All data files saved before this date
# have LED #0 controlling the cursor.
conds = pt[:, 3]
inds = np.nonzero((conds >= 0) & (conds != 4))
if len(inds[0]) > 0:
pt = pt[inds[0], :3]
#convert units from mm to cm and scale to desired amount
pt = pt.mean(0) * .1 * self.scale_factor
#ignore y direction
pt[1] = 0
#move cursor to marker location
self._update(pt)
else:
self.no_data_count += 1
else:
self.no_data_count += 1
#write to screen
self.draw_world()
def calc_trial_num(self):
'''Calculates the current trial count'''
trialtimes = [
state[1] for state in self.state_log
if state[0] in ['reward', 'timeout_penalty', 'hold_penalty']
]
return len(trialtimes)
def calc_rewards_per_min(self, window):
'''Calculates the Rewards/min for the most recent window of specified number of seconds in the past'''
rewardtimes = np.array(
[state[1] for state in self.state_log if state[0] == 'reward'])
if (self.get_time() - self.task_start_time) < window:
divideby = (self.get_time() - self.task_start_time) / 60.0
else:
divideby = window / 60.0
return np.sum(rewardtimes >= (self.get_time() - window)) / divideby
def calc_success_rate(self, window):
'''Calculates the rewarded trials/initiated trials for the most recent window of specified length in sec'''
trialtimes = np.array([
state[1] for state in self.state_log
if state[0] in ['reward', 'timeout_penalty', 'hold_penalty']
])
rewardtimes = np.array(
[state[1] for state in self.state_log if state[0] == 'reward'])
if len(trialtimes) == 0:
return 0.0
else:
return float(
np.sum(rewardtimes >= (self.get_time() - window))) / np.sum(
trialtimes >= (self.get_time() - window))
def update_report_stats(self):
'''Function to update any relevant report stats for the task. Values are saved in self.reportstats,
an ordered dictionary. Keys are strings that will be displayed as the label for the stat in the web interface,
values can be numbers or strings. Called every time task state changes.'''
super(TargetCapture, self).update_report_stats()
self.reportstats['Trial #'] = self.calc_trial_num()
self.reportstats['Reward/min'] = np.round(
self.calc_rewards_per_min(120), decimals=2)
self.reportstats['Success rate'] = str(
np.round(self.calc_success_rate(120) * 100.0, decimals=2)) + '%'
def _while_wait(self):
self.update_cursor()
def _while_origin(self):
self.update_cursor()
def _while_origin_hold(self):
self.update_cursor()
def _while_fixation_penalty(self):
self.update_cursor()
def _while_hold_penalty(self):
self.update_cursor()
def _while_reward(self):
self.update_cursor()
def _while_pre_target_change(self):
self.update_cursor()
def _while_target_change(self):
self.update_cursor()
def _pickle_init(self):
self.sphere = Sphere(radius=self.target_radius,
color=self.target_color)
self.graphics_models = [self.sphere]
self.sphere.translate(*self.position)
def __init__(self, **kwargs):
super(TestBoundary, self).__init__(**kwargs)
# Create a small sphere for each of the 6 boundary marks
self.xmin = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.xmin)
self.xmax = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.xmax)
self.ymin = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.ymin)
self.ymax = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.ymax)
self.zmin = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.zmin)
self.zmax = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.zmax)
class TentacleMultiConfigObstacleAvoidance(BMIJointPerturb):
status = dict(
wait=dict(start_trial="premove", stop=None),
premove=dict(premove_complete="target"),
target=dict(enter_target="hold",
timeout="timeout_penalty",
stop=None,
hit_obstacle="obstacle_penalty"),
hold=dict(leave_early="hold_penalty", hold_complete="targ_transition"),
targ_transition=dict(trial_complete="reward",
trial_abort="wait",
trial_incomplete="target",
trial_restart="premove"),
timeout_penalty=dict(timeout_penalty_end="targ_transition"),
hold_penalty=dict(hold_penalty_end="targ_transition"),
obstacle_penalty=dict(obstacle_penalty_end="targ_transition"),
reward=dict(reward_end="wait"))
obstacle_radius = traits.Float(2.0, desc='Radius of cylindrical obstacle')
obstacle_penalty = traits.Float(
0.0, desc='Penalty time if the chain hits the obstacle(s)')
def __init__(self, *args, **kwargs):
super(TentacleMultiConfigObstacleAvoidance,
self).__init__(*args, **kwargs)
## Create an obstacle object, hidden by default
self.obstacle = Sphere(radius=self.obstacle_radius + 0.6,
color=(0, 0, 1, .5))
self.obstacle_on = False
self.obstacle_pos = np.ones(3) * np.nan
self.hit_obstacle = False
self.add_model(self.obstacle)
def init(self):
self.add_dtype('obstacle_on', 'f8', (1, ))
self.add_dtype('obstacle_pos', 'f8', (3, ))
super(TentacleMultiConfigObstacleAvoidance, self).init()
def _cycle(self):
self.task_data['obstacle_on'] = self.obstacle_on
self.task_data['obstacle_pos'] = self.obstacle_pos
super(TentacleMultiConfigObstacleAvoidance, self)._cycle()
def _start_target(self):
super(TentacleMultiConfigObstacleAvoidance, self)._start_target()
if self.target_index == 1:
self.obstacle_pos = (self.targs[0] / 2)
self.obstacle.translate(*self.obstacle_pos, reset=True)
self.obstacle.attach()
self.obstacle_on = True
def _test_obstacle_penalty_end(self, ts):
return ts > self.obstacle_penalty
def _start_obstacle_penalty(self):
#hide targets
for target in self.targets:
target.hide()
self.tries += 1
self.target_index = -1
def _end_target(self):
self.obstacle.detach()
self.obstacle_on = False
def _test_hit_obstacle(self, ts):
if self.target_index == 1:
joint_angles = self.plant.get_intrinsic_coordinates()
distances_to_links = self.plant.kin_chain.detect_collision(
joint_angles, self.obstacle_pos)
hit = np.min(distances_to_links) < (self.obstacle_radius +
self.plant.link_radii[0])
if hit:
self.hit_obstacle = True
return True
else:
return False
@staticmethod
def tentacle_multi_start_config(nblocks=100,
ntargets=4,
distance=8,
startangle=45):
elbow_angles = np.array([
135, 180, 225
]) * np.pi / 180 # TODO make this a function argument!
startangle = 45 * np.pi / 180
n_configs_per_target = len(elbow_angles)
target_angles = np.arange(startangle, startangle + (2 * np.pi),
2 * np.pi / ntargets)
targets = distance * np.vstack(
[np.cos(target_angles), 0 * target_angles,
np.sin(target_angles)])
seq = []
from itertools import izip
import random
for i in range(nblocks):
target_inds = np.tile(np.arange(ntargets),
(n_configs_per_target, 1)).T.ravel()
config_inds = np.tile(np.arange(n_configs_per_target), ntargets)
sub_seq = []
inds = np.arange(n_configs_per_target * ntargets)
random.shuffle(inds)
for k in inds:
targ_ind = target_inds[k]
config_ind = config_inds[k]
seq_item = (np.vstack([targets[:, targ_ind],
np.zeros(3)]), elbow_angles[config_ind])
seq.append(seq_item)
return seq
class ManualControl2(ManualControl):
status = dict(wait=dict(start_trial="origin", stop=None),
origin=dict(enter_target="origin_hold", stop=None),
origin_hold=dict(leave_early="hold_penalty",
hold="terminus"),
terminus=dict(timeout="timeout_penalty",
enter_target="terminus_hold",
stop=None),
timeout_penalty=dict(penalty_end="pre_target_change"),
terminus_hold=dict(leave_early="hold_penalty",
hold="terminus2"),
terminus2=dict(timeout="timeout_penalty",
enter_target="terminus2_hold",
stop=None),
terminus2_hold=dict(leave_early="hold_penalty",
hold="reward"),
reward=dict(reward_end="target_change"),
hold_penalty=dict(penalty_end="pre_target_change"),
pre_target_change=dict(tried_enough='target_change',
not_tried_enough='wait'),
target_change=dict(target_change_end='wait'))
scale_factor = 2
cursor_radius = .4
def __init__(self, *args, **kwargs):
# Add the 2nd terminus target
super(ManualControl2, self).__init__(*args, **kwargs)
self.terminus2_target = Sphere(radius=self.terminus_size,
color=(1, 0, 0, .5))
self.add_model(self.terminus2_target)
def _start_wait(self):
#set target colors
self.terminus2_target.color = (1, 0, 0, .5)
#hide targets from previous trial
self.terminus2_target.detach()
super(ManualControl2, self)._start_wait()
def _test_enter_target(self, ts):
#get the current cursor location and target location, return true if center of cursor is inside target (has to be close enough to center to be fully inside)
if self.state == "terminus2":
c = self.cursor.xfm.move
t = self.terminus2_target.xfm.move
d = np.sqrt((c[0] - t[0])**2 + (c[1] - t[1])**2 + (c[2] - t[2])**2)
return d <= self.terminus_target.radius - self.cursor.radius
else:
return super(ManualControl2, self)._test_enter_target(ts)
def _start_origin(self):
if self.tries == 0:
#retrieve location of next terminus target
t2 = self.next_trial.T[2]
#move target to correct location
self.terminus2_target.translate(*t2, reset=True)
super(ManualControl2, self)._start_origin()
def _start_terminus_hold(self):
self.terminus2_target.color = (1, 0, 0, 0.5)
self.terminus2_target.attach()
self.requeue()
def _start_timeout_penalty(self):
#hide targets and fixation point
self.terminus2_target.detach()
super(ManualControl2, self)._start_timeout_penalty()
def _start_terminus2(self):
self.terminus_target.detach()
self.requeue()
def _test_leave_early(self, ts):
if self.state == "terminus2_hold":
c = self.cursor.xfm.move
t = self.terminus2_target.xfm.move
d = np.sqrt((c[0] - t[0])**2 + (c[1] - t[1])**2 + (c[2] - t[2])**2)
rad = self.terminus_target.radius - self.cursor.radius
return d > rad * self.exit_radius
else:
return super(ManualControl2, self)._test_leave_early(ts)
def _while_terminus2(self):
self.update_cursor()
def _while_terminus2_hold(self):
self.update_cursor()
def _end_terminus2_hold(self):
self.terminus2_target.color = (0, 1, 0, 0.5)
def _start_hold_penalty(self):
self.terminus2_target.detach()
super(ManualControl2, self)._start_hold_penalty()
def _start_timeout_penalty(self):
self.terminus2_target.detach()
super(ManualControl2, self)._start_timeout_penalty()
def update_target_location(self):
# Determine the task target for assist/decoder adaptation purposes (convert
# units from cm to mm for decoder)
# TODO - decide what to do with y location, target_xz ignores it!
if self.state == 'terminus2' or self.state == 'terminus2_hold':
self.location = 10 * self.terminus2_target.xfm.move
self.target_xz = np.array([self.location[0], self.location[2]])
super(ManualControl2, self).update_target_location()
def __init__(self, *args, **kwargs):
# Add the 2nd terminus target
super(ManualControl2, self).__init__(*args, **kwargs)
self.terminus2_target = Sphere(radius=self.terminus_size,
color=(1, 0, 0, .5))
self.add_model(self.terminus2_target)
def __init__(self, **kwargs):
super(MovementTraining, self).__init__(**kwargs)
self.cursor = Sphere(radius=.5, color=(.5, 0, .5, 1))
self.add_model(self.cursor)
class ManualControl(TargetCapture):
status = dict(wait=dict(start_trial="origin", stop=None),
origin=dict(enter_target="origin_hold", stop=None),
origin_hold=dict(leave_early="hold_penalty",
hold="terminus"),
terminus=dict(timeout="timeout_penalty",
enter_target="terminus_hold",
stop=None),
timeout_penalty=dict(penalty_end="pre_target_change"),
terminus_hold=dict(leave_early="hold_penalty",
hold="reward"),
reward=dict(reward_end="target_change"),
hold_penalty=dict(penalty_end="pre_target_change"),
pre_target_change=dict(tried_enough='target_change',
not_tried_enough='wait'),
target_change=dict(target_change_end='wait'))
#create settable traits
terminus_size = traits.Float(1, desc="Radius of terminus targets")
terminus_hold_time = traits.Float(
2, desc="Length of hold required at terminus")
timeout_time = traits.Float(
10, desc="Time allowed to go between origin and terminus")
timeout_penalty_time = traits.Float(
3, desc="Length of penalty time for timeout error")
#create fixation point, targets, cursor objects, initialize
def __init__(self, *args, **kwargs):
# Add the target and cursor locations to the task data to be saved to
# file
self.dtype = [('target', 'f', (3, )), ('cursor', 'f', (3, ))]
super(ManualControl, self).__init__(*args, **kwargs)
self.terminus_target = Sphere(radius=self.terminus_size,
color=(1, 0, 0, .5))
self.add_model(self.terminus_target)
# Initialize target location variables
self.location = np.array([0, 0, 0])
self.target_xz = np.array([0, 0])
def _start_wait(self):
super(ManualControl, self)._start_wait()
#set target colors
self.terminus_target.color = (1, 0, 0, .5)
#hide targets from previous trial
self.show_terminus(False)
def _start_origin(self):
if self.tries == 0:
#retrieve location of next terminus target
t = self.next_trial.T[1]
#move target to correct location
self.terminus_target.translate(*t, reset=True)
super(ManualControl, self)._start_origin()
def _start_origin_hold(self):
#make terminus target visible
self.show_terminus(True)
def show_terminus(self, show=False):
if show:
self.terminus_target.attach()
else:
self.terminus_target.detach()
self.requeue()
def _start_terminus(self):
self.show_origin(False)
def _end_terminus_hold(self):
self.terminus_target.color = (0, 1, 0, 0.5)
def _start_hold_penalty(self):
#hide targets
super(ManualControl, self)._start_hold_penalty()
self.show_terminus(False)
def _start_timeout_penalty(self):
#hide targets and fixation point
self.tries += 1
self.show_terminus(False)
def _start_reward(self):
pass
def _test_enter_target(self, ts):
#get the current cursor location and target location, return true if center of cursor is inside target (has to be close enough to center to be fully inside)
if self.state == "origin":
c = self.cursor.xfm.move
t = self.origin_target.xfm.move
d = np.sqrt((c[0] - t[0])**2 + (c[1] - t[1])**2 + (c[2] - t[2])**2)
return d <= self.origin_target.radius - self.cursor.radius
if self.state == "terminus":
c = self.cursor.xfm.move
t = self.terminus_target.xfm.move
d = np.sqrt((c[0] - t[0])**2 + (c[1] - t[1])**2 + (c[2] - t[2])**2)
return d <= self.terminus_target.radius - self.cursor.radius
def _test_leave_early(self, ts):
if self.state == "origin_hold":
c = self.cursor.xfm.move
t = self.origin_target.xfm.move
d = np.sqrt((c[0] - t[0])**2 + (c[1] - t[1])**2 + (c[2] - t[2])**2)
rad = self.origin_target.radius - self.cursor.radius
return d > rad * self.exit_radius
if self.state == "terminus_hold":
c = self.cursor.xfm.move
t = self.terminus_target.xfm.move
d = np.sqrt((c[0] - t[0])**2 + (c[1] - t[1])**2 + (c[2] - t[2])**2)
rad = self.terminus_target.radius - self.cursor.radius
return d > rad * self.exit_radius
def _test_hold(self, ts):
if self.state == "origin_hold":
return ts >= self.origin_hold_time
else:
return ts >= self.terminus_hold_time
def _test_timeout(self, ts):
return ts > self.timeout_time
def _test_penalty_end(self, ts):
if self.state == "timeout_penalty":
return ts > self.timeout_penalty_time
if self.state == "fixation_penalty":
return ts > self.fixation_penalty_time
else:
return ts > self.hold_penalty_time
def _while_terminus(self):
self.update_cursor()
def _while_terminus_hold(self):
self.update_cursor()
def _while_timeout_penalty(self):
self.update_cursor()
def update_target_location(self):
# Determine the task target for assist/decoder adaptation purposes (convert
# units from cm to mm for decoder)
# TODO - decide what to do with y location, target_xz ignores it!
if self.state == 'origin' or self.state == 'origin_hold':
self.location = 10 * self.origin_target.xfm.move
self.target_xz = np.array([self.location[0], self.location[2]])
elif self.state == 'terminus' or self.state == 'terminus_hold':
self.location = 10 * self.terminus_target.xfm.move
self.target_xz = np.array([self.location[0], self.location[2]])
self.task_data['target'] = self.location[:3]
def update_cursor(self):
self.update_target_location()
super(ManualControl, self).update_cursor()
self.task_data['cursor'] = self.cursor.xfm.move.copy()
from riglib.stereo_opengl.primitives import Cylinder, Plane, Sphere, Cone
from riglib.stereo_opengl.models import FlatMesh, Group
from riglib.stereo_opengl.textures import Texture, TexModel
from riglib.stereo_opengl.render import ssao, stereo, Renderer
from riglib.stereo_opengl.utils import cloudy_tex
from riglib.stereo_opengl.ik import RobotArmGen2D
from riglib.stereo_opengl.xfm import Quaternion
import time
from riglib.stereo_opengl.ik import RobotArm
import pygame
arm4j = RobotArmGen2D(link_radii=.2, joint_radii=.2, link_lengths=[4, 4, 2, 2])
cone = Sphere(radius=1)
pos_list = np.array([[0, 0, 0], [0, 0, 5]])
class Test2(Window):
def __init__(self, *args, **kwargs):
self.count = 0
super(Test2, self).__init__(*args, **kwargs)
def _start_draw(self):
#arm4j.set_joint_pos([0,0,np.pi/2,np.pi/2])
#arm4j.get_endpoint_pos()
pass
def _while_draw(self):
def __init__(self, body_weight=6.5, base_loc=np.array([2., 0., -15])):
'''
body_weight : float
Entire weight of subject in kg. Used to determine the mass of the arm segements using regression model from Cheng & Scott 2000, p221, Table 8
'''
# Initialize the dynamics world
# world = ode.World() # TODO this should be part of the window, for object collision detection stuff
# world.setGravity((0,0,0))
# Arm link lengths----from monkey P? Numbers taken from MATLAB code originally written by Rodolphe Heliot/Amy Orsborn
# Changed to these values because most common among old code. Cheng & Scott 2000 Table 2 has other values if change needed
self.l_ua = 17.70 # cm
self.l_fa = 20.35 # cm
# Friction coefficients
self.B = np.mat([[0.03, 0.01],
[0.01, 0.03]])
# Mass of upperarm/forearm from Cheng & Scott, 2000, p221, Table 8 (based on morphometric data)
self.m_ua = 0.001*(23 + 34.4*body_weight)
self.m_fa = 0.001*(53 + 25.2*body_weight)
## Determine the inertia of each segment
rad_of_gyration = np.array([0.247, 0.248]) # relative to the length of each segment
# Calculate center of mass for each segment
self.ctr_of_mass_ua = self.l_ua * rad_of_gyration[0]
self.ctr_of_mass_fa = self.l_fa * rad_of_gyration[1]
self.r_ua = self.ctr_of_mass_ua
self.r_fa = self.ctr_of_mass_fa
# Calculate moment of inertia for each segment
# i = 0.001 * 0.0001 * (b + m*total_body_weight), where 'b' and 'm' are from Cheng & Scott 2000, p221, Table 8
# 0.001 * 0.0001 converts (g cm^2) ==> (kg m^2)
self.I_ua = 0.001*0.0001*(432 + 356.6*body_weight)
self.I_fa = 0.001*0.0001*(2381 + 861.6*body_weight)
self.rad_ua = np.sqrt(4*(self.I_ua/self.m_ua - 1./3*(0.01*self.l_ua)**2))
self.rad_fa = np.sqrt(4*(self.I_fa/self.m_fa - 1./3*(0.01*self.l_fa)**2))
# Create two bodies
# upper_arm = ode.Body(world)
# M = ode.Mass()
# M.setCylinderTotal(total_mass=100*self.m_ua, direction=1, r=3, h=self.l_ua)
# upper_arm.setMass(M)
# upper_arm.setPosition(base_loc + np.array([self.l_ua, 0, 0]))
# forearm = ode.Body(world)
# M = ode.Mass()
# M.setCylinderTotal(total_mass=100*self.m_fa, direction=1, r=3, h=self.l_fa)
# forearm.setMass(M)
# forearm.setPosition(base_loc + np.array([self.l_ua + self.l_fa, 0, 0]))
# # anchor upper_arm to the world at position (2., 0, -15)
# j1 = ode.HingeJoint(world)
# j1.attach(upper_arm, ode.environment)
# j1.setAnchor(base_loc)
# j1.setAxis((0, 1, 0))
# # anchor forearm to the distal end of upper_arm
# j2 = ode.HingeJoint(world)
# j2.attach(upper_arm, forearm)
# j2.setAnchor(base_loc + np.array([self.l_ua, 0, 0]))
# j2.setAxis((0, 1, 0))
# self.arm_segments = [upper_arm, forearm]
# self.joints = [j1, j2]
# self.world = world
# self.num_joints = len(self.joints)
self.theta = np.array([ 0.38118002, 2.08145271])# angular
self.omega = np.zeros(2) # angular vel
self.alpha = np.zeros(2) # angular acc
self.torque = np.zeros(2)
self.base_loc = base_loc
link_radii=arm_radius
joint_radii=arm_radius
joint_colors=arm_color
link_colors=arm_color
self.link_lengths = link_lengths = [self.l_ua, self.l_fa]
self.num_joints = len(self.link_lengths)
self.curr_vecs = np.zeros([self.num_joints, 3]) #rows go from proximal to distal links
self.chain = Chain(link_radii, joint_radii, link_lengths, joint_colors, link_colors)
self.cursor = Sphere(radius=arm_radius/2, color=link_colors)
self.graphics_models = [self.chain.link_groups[0], self.cursor]
self.chain.translate(*self.base_loc, reset=True)
self.kin_chain = robot_arms.PlanarXZKinematicChain2Link(link_lengths, base_loc=base_loc)
self.stay_on_screen = False
self.visible = True
class ApproachAvoidanceTask(Sequence, Window):
'''
This is for a free-choice task with two targets (left and right) presented to choose from.
The position of the targets may change along the x-axis, according to the target generator,
and each target has a varying probability of reward, also according to the target generator.
The code as it is written is for a joystick.
Notes: want target_index to only write once per trial. if so, can make instructed trials random. else, make new state for instructed trial.
'''
background = (0,0,0,1)
shoulder_anchor = np.array([2., 0., -15.]) # Coordinates of shoulder anchor point on screen
arm_visible = traits.Bool(True, desc='Specifies whether entire arm is displayed or just endpoint')
cursor_radius = traits.Float(.5, desc="Radius of cursor")
cursor_color = (.5,0,.5,1)
joystick_method = traits.Float(1,desc="1: Normal velocity, 0: Position control")
joystick_speed = traits.Float(20, desc="Speed of cursor")
plant_type_options = plantlist.keys()
plant_type = traits.OptionsList(*plantlist, bmi3d_input_options=plantlist.keys())
starting_pos = (5, 0, 5)
# window_size = (1280*2, 1024)
window_size = traits.Tuple((1366*2, 768), desc='window size')
status = dict(
#wait = dict(start_trial="target", stop=None),
wait = dict(start_trial="center", stop=None),
center = dict(enter_center="hold_center", timeout="timeout_penalty", stop=None),
hold_center = dict(leave_early_center = "hold_penalty",hold_center_complete="target", timeout="timeout_penalty", stop=None),
target = dict(enter_targetL="hold_targetL", enter_targetH = "hold_targetH", timeout="timeout_penalty", stop=None),
hold_targetR = dict(leave_early_R="hold_penalty", hold_complete="targ_transition"),
hold_targetL = dict(leave_early_L="hold_penalty", hold_complete="targ_transition"),
targ_transition = dict(trial_complete="check_reward",trial_abort="wait", trial_incomplete="center"),
check_reward = dict(avoid="reward",approach="reward_and_airpuff"),
timeout_penalty = dict(timeout_penalty_end="targ_transition"),
hold_penalty = dict(hold_penalty_end="targ_transition"),
reward = dict(reward_end="wait"),
reward_and_airpuff = dict(reward_and_airpuff_end="wait"),
)
#
target_color = (.5,1,.5,0)
#initial state
state = "wait"
#create settable traits
reward_time_avoid = traits.Float(.2, desc="Length of juice reward for avoid decision")
reward_time_approach_min = traits.Float(.2, desc="Min length of juice for approach decision")
reward_time_approach_max = traits.Float(.8, desc="Max length of juice for approach decision")
target_radius = traits.Float(1.5, desc="Radius of targets in cm")
block_length = traits.Float(100, desc="Number of trials per block")
hold_time = traits.Float(.5, desc="Length of hold required at targets")
hold_penalty_time = traits.Float(1, desc="Length of penalty time for target hold error")
timeout_time = traits.Float(10, desc="Time allowed to go between targets")
timeout_penalty_time = traits.Float(1, desc="Length of penalty time for timeout error")
max_attempts = traits.Int(10, desc='The number of attempts at a target before\
skipping to the next one')
session_length = traits.Float(0, desc="Time until task automatically stops. Length of 0 means no auto stop.")
marker_num = traits.Int(14, desc="The index of the motiontracker marker to use for cursor position")
arm_hide_rate = traits.Float(0.0, desc='If the arm is visible, specifies a percentage of trials where it will be hidden')
target_index = 0 # Helper variable to keep track of whether trial is instructed (1 = 1 choice) or free-choice (2 = 2 choices)
target_selected = 'L' # Helper variable to indicate which target was selected
tries = 0 # Helper variable to keep track of the number of failed attempts at a given trial.
timedout = False # Helper variable to keep track if transitioning from timeout_penalty
reward_counter = 0.0
cursor_visible = False # Determines when to hide the cursor.
no_data_count = 0 # Counter for number of missing data frames in a row
scale_factor = 3.0 #scale factor for converting hand movement to screen movement (1cm hand movement = 3.5cm cursor movement)
starting_dist = 10.0 # starting distance from center target
#color_targets = np.random.randint(2)
color_targets = 1 # 0: yellow low, blue high; 1: blue low, yellow high
stopped_center_hold = False #keep track if center hold was released early
limit2d = 1
color1 = target_colors['purple'] # approach color
color2 = target_colors['lightsteelblue'] # avoid color
reward_color = target_colors['green'] # color of reward bar
airpuff_color = target_colors['red'] # color of airpuff bar
sequence_generators = ['colored_targets_with_probabilistic_reward','block_probabilistic_reward','colored_targets_with_randomwalk_reward','randomwalk_probabilistic_reward']
def __init__(self, *args, **kwargs):
super(ApproachAvoidanceTask, self).__init__(*args, **kwargs)
self.cursor_visible = True
# Add graphics models for the plant and targets to the window
self.plant = plantlist[self.plant_type]
self.plant_vis_prev = True
# Add graphics models for the plant and targets to the window
if hasattr(self.plant, 'graphics_models'):
for model in self.plant.graphics_models:
self.add_model(model)
self.current_pt=np.zeros([3]) #keep track of current pt
self.last_pt=np.zeros([3]) #kee
## Declare cursor
#self.dtype.append(('cursor', 'f8', (3,)))
if 0: #hasattr(self.arm, 'endpt_cursor'):
self.cursor = self.arm.endpt_cursor
else:
self.cursor = Sphere(radius=self.cursor_radius, color=self.cursor_color)
self.add_model(self.cursor)
self.cursor.translate(*self.get_arm_endpoint(), reset=True)
## Instantiate the targets. Target 1 is center target, Target H is target with high probability of reward, Target L is target with low probability of reward.
self.target1 = Sphere(radius=self.target_radius, color=self.target_color) # center target
self.add_model(self.target1)
self.targetR = Sphere(radius=self.target_radius, color=self.target_color) # left target
self.add_model(self.targetH)
self.targetL = Sphere(radius=self.target_radius, color=self.target_color) # right target
self.add_model(self.targetL)
###STOPPED HERE: should define Rect target here and then adapt length during task. Also,
### be sure to change all targetH instantiations to targetR.
# Initialize target location variable.
self.target_location1 = np.array([0,0,0])
self.target_locationR = np.array([-self.starting_dist,0,0])
self.target_locationL = np.array([self.starting_dist,0,0])
self.target1.translate(*self.target_location1, reset=True)
self.targetH.translate(*self.target_locationR, reset=True)
self.targetL.translate(*self.target_locationL, reset=True)
# Initialize colors for high probability and low probability target. Color will not change.
self.targetH.color = self.color_targets*self.color1 + (1 - self.color_targets)*self.color2 # high is magenta if color_targets = 1, juicyorange otherwise
self.targetL.color = (1 - self.color_targets)*self.color1 + self.color_targets*self.color2
#set target colors
self.target1.color = (1,0,0,.5) # center target red
# Initialize target location variable
self.target_location = np.array([0, 0, 0])
# Declare any plant attributes which must be saved to the HDF file at the _cycle rate
for attr in self.plant.hdf_attrs:
self.add_dtype(*attr)
def init(self):
self.add_dtype('targetR', 'f8', (3,))
self.add_dtype('targetL','f8', (3,))
self.add_dtype('reward_scheduleR','f8', (1,))
self.add_dtype('reward_scheduleL','f8', (1,))
self.add_dtype('target_index', 'i', (1,))
super(ApproachAvoidanceTask, self).init()
self.trial_allocation = np.zeros(1000)
def _cycle(self):
''' Calls any update functions necessary and redraws screen. Runs 60x per second. '''
## Run graphics commands to show/hide the arm if the visibility has changed
if self.plant_type != 'cursor_14x14':
if self.arm_visible != self.arm_vis_prev:
self.arm_vis_prev = self.arm_visible
self.show_object(self.arm, show=self.arm_visible)
self.move_arm()
#self.move_plant()
## Save plant status to HDF file
plant_data = self.plant.get_data_to_save()
for key in plant_data:
self.task_data[key] = plant_data[key]
self.update_cursor()
if self.plant_type != 'cursor_14x14':
self.task_data['joint_angles'] = self.get_arm_joints()
super(ApproachAvoidanceTask, self)._cycle()
## Plant functions
def get_cursor_location(self):
# arm returns it's position as if it was anchored at the origin, so have to translate it to the correct place
return self.get_arm_endpoint()
def get_arm_endpoint(self):
return self.plant.get_endpoint_pos()
def set_arm_endpoint(self, pt, **kwargs):
self.plant.set_endpoint_pos(pt, **kwargs)
def set_arm_joints(self, angles):
self.arm.set_intrinsic_coordinates(angles)
def get_arm_joints(self):
return self.arm.get_intrinsic_coordinates()
def update_cursor(self):
'''
Update the cursor's location and visibility status.
'''
pt = self.get_cursor_location()
self.update_cursor_visibility()
if pt is not None:
self.move_cursor(pt)
def move_cursor(self, pt):
''' Move the cursor object to the specified 3D location. '''
# if not hasattr(self.arm, 'endpt_cursor'):
self.cursor.translate(*pt[:3],reset=True)
##
##### HELPER AND UPDATE FUNCTIONS ####
def move_arm(self):
''' Returns the 3D coordinates of the cursor. For manual control, uses
joystick data. If no joystick data available, returns None'''
pt = self.joystick.get()
if len(pt) > 0:
pt = pt[-1][0]
pt[0]=1-pt[0]; #Switch L / R axes
calib = [0.497,0.517] #Sometimes zero point is subject to drift this is the value of the incoming joystick when at 'rest'
if self.joystick_method==0:
pos = np.array([(pt[0]-calib[0]), 0, calib[1]-pt[1]])
pos[0] = pos[0]*36
pos[2] = pos[2]*24
self.current_pt = pos
elif self.joystick_method==1:
vel=np.array([(pt[0]-calib[0]), 0, calib[1]-pt[1]])
epsilon = 2*(10**-2) #Define epsilon to stabilize cursor movement
if sum((vel)**2) > epsilon:
self.current_pt=self.last_pt+self.joystick_speed*vel*(1/60) #60 Hz update rate, dt = 1/60
else:
self.current_pt = self.last_pt
if self.current_pt[0] < -25: self.current_pt[0] = -25
if self.current_pt[0] > 25: self.current_pt[0] = 25
if self.current_pt[-1] < -14: self.current_pt[-1] = -14
if self.current_pt[-1] > 14: self.current_pt[-1] = 14
self.set_arm_endpoint(self.current_pt)
self.last_pt = self.current_pt.copy()
def convert_to_cm(self, val):
return val/10.0
def update_cursor_visibility(self):
''' Update cursor visible flag to hide cursor if there has been no good data for more than 3 frames in a row'''
prev = self.cursor_visible
if self.no_data_count < 3:
self.cursor_visible = True
if prev != self.cursor_visible:
self.show_object(self.cursor, show=True)
self.requeue()
else:
self.cursor_visible = False
if prev != self.cursor_visible:
self.show_object(self.cursor, show=False)
self.requeue()
def calc_n_successfultrials(self):
trialendtimes = np.array([state[1] for state in self.state_log if state[0]=='check_reward'])
return len(trialendtimes)
def calc_n_rewards(self):
rewardtimes = np.array([state[1] for state in self.state_log if state[0]=='reward'])
return len(rewardtimes)
def calc_trial_num(self):
'''Calculates the current trial count: completed + aborted trials'''
trialtimes = [state[1] for state in self.state_log if state[0] in ['wait']]
return len(trialtimes)-1
def calc_targetH_num(self):
'''Calculates the total number of times the high-value target was selected'''
trialtimes = [state[1] for state in self.state_log if state[0] in ['hold_targetH']]
return len(trialtimes) - 1
def calc_rewards_per_min(self, window):
'''Calculates the Rewards/min for the most recent window of specified number of seconds in the past'''
rewardtimes = np.array([state[1] for state in self.state_log if state[0]=='reward'])
if (self.get_time() - self.task_start_time) < window:
divideby = (self.get_time() - self.task_start_time)/sec_per_min
else:
divideby = window/sec_per_min
return np.sum(rewardtimes >= (self.get_time() - window))/divideby
def calc_success_rate(self, window):
'''Calculates the rewarded trials/initiated trials for the most recent window of specified length in sec'''
trialtimes = np.array([state[1] for state in self.state_log if state[0] in ['reward', 'timeout_penalty', 'hold_penalty']])
rewardtimes = np.array([state[1] for state in self.state_log if state[0]=='reward'])
if len(trialtimes) == 0:
return 0.0
else:
return float(np.sum(rewardtimes >= (self.get_time() - window)))/np.sum(trialtimes >= (self.get_time() - window))
def update_report_stats(self):
'''Function to update any relevant report stats for the task. Values are saved in self.reportstats,
an ordered dictionary. Keys are strings that will be displayed as the label for the stat in the web interface,
values can be numbers or strings. Called every time task state changes.'''
super(ApproachAvoidanceTask, self).update_report_stats()
self.reportstats['Trial #'] = self.calc_trial_num()
self.reportstats['Reward/min'] = np.round(self.calc_rewards_per_min(120),decimals=2)
self.reportstats['High-value target selections'] = self.calc_targetH_num()
#self.reportstats['Success rate'] = str(np.round(self.calc_success_rate(120)*100.0,decimals=2)) + '%'
start_time = self.state_log[0][1]
rewardtimes=np.array([state[1] for state in self.state_log if state[0]=='reward'])
if len(rewardtimes):
rt = rewardtimes[-1]-start_time
else:
rt= np.float64("0.0")
sec = str(np.int(np.mod(rt,60)))
if len(sec) < 2:
sec = '0'+sec
self.reportstats['Time Of Last Reward'] = str(np.int(np.floor(rt/60))) + ':' + sec
#### TEST FUNCTIONS ####
def _test_enter_center(self, ts):
#return true if the distance between center of cursor and target is smaller than the cursor radius
d = np.sqrt((self.cursor.xfm.move[0]-self.target_location1[0])**2 + (self.cursor.xfm.move[1]-self.target_location1[1])**2 + (self.cursor.xfm.move[2]-self.target_location1[2])**2)
#print 'TARGET SELECTED', self.target_selected
return d <= self.target_radius - self.cursor_radius
def _test_enter_targetL(self, ts):
if self.target_index == 1 and self.LH_target_on[0]==0:
#return false if instructed trial and this target is not on
return False
else:
#return true if the distance between center of cursor and target is smaller than the cursor radius
d = np.sqrt((self.cursor.xfm.move[0]-self.target_locationL[0])**2 + (self.cursor.xfm.move[1]-self.target_locationL[1])**2 + (self.cursor.xfm.move[2]-self.target_locationL[2])**2)
self.target_selected = 'L'
#print 'TARGET SELECTED', self.target_selected
return d <= self.target_radius - self.cursor_radius
def _test_enter_targetH(self, ts):
if self.target_index ==1 and self.LH_target_on[1]==0:
return False
else:
#return true if the distance between center of cursor and target is smaller than the cursor radius
d = np.sqrt((self.cursor.xfm.move[0]-self.target_locationH[0])**2 + (self.cursor.xfm.move[1]-self.target_locationH[1])**2 + (self.cursor.xfm.move[2]-self.target_locationH[2])**2)
self.target_selected = 'H'
#print 'TARGET SELECTED', self.target_selected
return d <= self.target_radius - self.cursor_radius
def _test_leave_early_center(self, ts):
# return true if cursor moves outside the exit radius (gives a bit of slack around the edge of target once cursor is inside)
d = np.sqrt((self.cursor.xfm.move[0]-self.target_location1[0])**2 + (self.cursor.xfm.move[1]-self.target_location1[1])**2 + (self.cursor.xfm.move[2]-self.target_location1[2])**2)
rad = self.target_radius - self.cursor_radius
return d > rad
def _test_leave_early_L(self, ts):
# return true if cursor moves outside the exit radius (gives a bit of slack around the edge of target once cursor is inside)
d = np.sqrt((self.cursor.xfm.move[0]-self.target_locationL[0])**2 + (self.cursor.xfm.move[1]-self.target_locationL[1])**2 + (self.cursor.xfm.move[2]-self.target_locationL[2])**2)
rad = self.target_radius - self.cursor_radius
return d > rad
def _test_leave_early_H(self, ts):
# return true if cursor moves outside the exit radius (gives a bit of slack around the edge of target once cursor is inside)
d = np.sqrt((self.cursor.xfm.move[0]-self.target_locationH[0])**2 + (self.cursor.xfm.move[1]-self.target_locationH[1])**2 + (self.cursor.xfm.move[2]-self.target_locationH[2])**2)
rad = self.target_radius - self.cursor_radius
return d > rad
def _test_hold_center_complete(self, ts):
return ts>=self.hold_time
def _test_hold_complete(self, ts):
return ts>=self.hold_time
def _test_timeout(self, ts):
return ts>self.timeout_time
def _test_timeout_penalty_end(self, ts):
return ts>self.timeout_penalty_time
def _test_hold_penalty_end(self, ts):
return ts>self.hold_penalty_time
def _test_trial_complete(self, ts):
#return self.target_index==self.chain_length-1
return not self.timedout
def _test_trial_incomplete(self, ts):
return (not self._test_trial_complete(ts)) and (self.tries<self.max_attempts)
def _test_trial_abort(self, ts):
return (not self._test_trial_complete(ts)) and (self.tries==self.max_attempts)
def _test_yes_reward(self,ts):
if self.target_selected == 'H':
#reward_assigned = self.targs[0,1]
reward_assigned = self.rewardH
else:
#reward_assigned = self.targs[1,1]
reward_assigned = self.rewardL
if self.reward_SmallLarge==1:
self.reward_time = reward_assigned*self.reward_time_large + (1 - reward_assigned)*self.reward_time_small # update reward time if using Small/large schedule
reward_assigned = 1 # always rewarded
return bool(reward_assigned)
def _test_no_reward(self,ts):
if self.target_selected == 'H':
#reward_assigned = self.targs[0,1]
reward_assigned = self.rewardH
else:
#reward_assigned = self.targs[1,1]
reward_assigned = self.rewardL
if self.reward_SmallLarge==True:
self.reward_time = reward_assigned*self.reward_time_large + (1 - reward_assigned)*self.reward_time_small # update reward time if using Small/large schedule
reward_assigned = 1 # always rewarded
return bool(not reward_assigned)
def _test_reward_end(self, ts):
time_ended = (ts > self.reward_time)
self.reward_counter = self.reward_counter + 1
return time_ended
def _test_stop(self, ts):
if self.session_length > 0 and (time.time() - self.task_start_time) > self.session_length:
self.end_task()
return self.stop
#### STATE FUNCTIONS ####
def show_object(self, obj, show=False):
'''
Show or hide an object
'''
if show:
obj.attach()
else:
obj.detach()
self.requeue()
def _start_wait(self):
super(ApproachAvoidanceTask, self)._start_wait()
self.tries = 0
self.target_index = 0 # indicator for instructed or free-choice trial
#hide targets
self.show_object(self.target1, False)
self.show_object(self.targetL, False)
self.show_object(self.targetH, False)
#get target positions and reward assignments for this trial
self.targs = self.next_trial
if self.plant_type != 'cursor_14x14' and np.random.rand() < self.arm_hide_rate:
self.arm_visible = False
else:
self.arm_visible = True
#self.chain_length = self.targs.shape[0] #Number of sequential targets in a single trial
#self.task_data['target'] = self.target_locationH.copy()
assign_reward = np.random.randint(0,100,size=2)
self.rewardH = np.greater(self.targs[0,1],assign_reward[0])
#print 'high value target reward prob', self.targs[0,1]
self.rewardL = np.greater(self.targs[1,1],assign_reward[1])
#print 'TARGET GENERATOR', self.targs[0,]
self.task_data['targetH'] = self.targs[0,].copy()
self.task_data['reward_scheduleH'] = self.rewardH.copy()
self.task_data['targetL'] = self.targs[1,].copy()
self.task_data['reward_scheduleL'] = self.rewardL.copy()
self.requeue()
def _start_center(self):
#self.target_index += 1
self.show_object(self.target1, True)
self.show_object(self.cursor, True)
# Third argument in self.targs determines if target is on left or right
# First argument in self.targs determines if location is offset to farther distances
offsetH = (2*self.targs[0,2] - 1)*(self.starting_dist + self.location_offset_allowed*self.targs[0,0]*4.0)
moveH = np.array([offsetH,0,0])
offsetL = (2*self.targs[1,2] - 1)*(self.starting_dist + self.location_offset_allowed*self.targs[1,0]*4.0)
moveL = np.array([offsetL,0,0])
self.targetL.translate(*moveL, reset=True)
#self.targetL.move_to_position(*moveL, reset=True)
##self.targetL.translate(*self.targs[self.target_index], reset=True)
self.show_object(self.targetL, True)
self.target_locationL = self.targetL.xfm.move
self.targetH.translate(*moveH, reset=True)
#self.targetR.move_to_position(*moveR, reset=True)
##self.targetR.translate(*self.targs[self.target_index], reset=True)
self.show_object(self.targetH, True)
self.target_locationH = self.targetH.xfm.move
# Insert instructed trials within free choice trials
if self.trial_allocation[self.calc_trial_num()] == 1:
#if (self.calc_trial_num() % 10) < (self.percentage_instructed_trials/10):
self.target_index = 1 # instructed trial
leftright_coinflip = np.random.randint(0,2)
if leftright_coinflip == 0:
self.show_object(self.targetL, False)
self.LH_target_on = (0, 1)
else:
self.show_object(self.targetH, False)
self.LR_coinflip = 0
self.LH_target_on = (1, 0)
else:
self.target_index = 2 # free-choice trial
self.cursor_visible = True
self.task_data['target_index'] = self.target_index
self.requeue()
def _start_target(self):
#self.target_index += 1
#move targets to current location and set location attribute. Target1 (center target) position does not change.
self.show_object(self.target1, False)
#self.target_location1 = self.target1.xfm.move
self.show_object(self.cursor, True)
self.update_cursor()
self.requeue()
def _start_hold_center(self):
self.show_object(self.target1, True)
self.timedout = False
self.requeue()
def _start_hold_targetL(self):
#make next target visible unless this is the final target in the trial
#if 1 < self.chain_length:
#self.targetL.translate(*self.targs[self.target_index+1], reset=True)
# self.show_object(self.targetL, True)
# self.requeue()
self.show_object(self.targetL, True)
self.timedout = False
self.requeue()
def _start_hold_targetH(self):
#make next target visible unless this is the final target in the trial
#if 1 < self.chain_length:
#self.targetR.translate(*self.targs[self.target_index+1], reset=True)
# self.show_object(self.targetR, True)
# self.requeue()
self.show_object(self.targetH, True)
self.timedout = False
self.requeue()
def _end_hold_center(self):
self.target1.radius = 0.7*self.target_radius # color target green
def _end_hold_targetL(self):
self.targetL.color = (0,1,0,0.5) # color target green
def _end_hold_targetH(self):
self.targetH.color = (0,1,0,0.5) # color target green
def _start_hold_penalty(self):
#hide targets
self.show_object(self.target1, False)
self.show_object(self.targetL, False)
self.show_object(self.targetH, False)
self.timedout = True
self.requeue()
self.tries += 1
#self.target_index = -1
def _start_timeout_penalty(self):
#hide targets
self.show_object(self.target1, False)
self.show_object(self.targetL, False)
self.show_object(self.targetH, False)
self.timedout = True
self.requeue()
self.tries += 1
#self.target_index = -1
def _start_targ_transition(self):
#hide targets
self.show_object(self.target1, False)
self.show_object(self.targetL, False)
self.show_object(self.targetH, False)
self.requeue()
def _start_check_reward(self):
#hide targets
self.show_object(self.target1, False)
self.show_object(self.targetL, False)
self.show_object(self.targetH, False)
self.requeue()
def _start_reward(self):
#super(ApproachAvoidanceTask, self)._start_reward()
if self.target_selected == 'L':
self.show_object(self.targetL, True)
#reward_assigned = self.targs[1,1]
else:
self.show_object(self.targetH, True)
#reward_assigned = self.targs[0,1]
#self.reward_counter = self.reward_counter + float(reward_assigned)
self.requeue()
@staticmethod
def colored_targets_with_probabilistic_reward(length=1000, boundaries=(-18,18,-10,10,-15,15),reward_high_prob=80,reward_low_prob=40):
"""
Generator should return array of ntrials x 2 x 3. The second dimension is for each target.
For example, first is the target with high probability of reward, and the second
entry is for the target with low probability of reward. The third dimension holds three variables indicating
position offset (yes/no), reward probability (fixed in this case), and location (binary returned where the
ouput indicates either left or right).
UPDATE: CHANGED SO THAT THE SECOND DIMENSION CARRIES THE REWARD PROBABILITY RATHER THAN THE REWARD SCHEDULE
"""
position_offsetH = np.random.randint(2,size=(1,length))
position_offsetL = np.random.randint(2,size=(1,length))
location_int = np.random.randint(2,size=(1,length))
# coin flips for reward schedules, want this to be elementwise comparison
#assign_rewardH = np.random.randint(0,100,size=(1,length))
#assign_rewardL = np.random.randint(0,100,size=(1,length))
high_prob = reward_high_prob*np.ones((1,length))
low_prob = reward_low_prob*np.ones((1,length))
#reward_high = np.greater(high_prob,assign_rewardH)
#reward_low = np.greater(low_prob,assign_rewardL)
pairs = np.zeros([length,2,3])
pairs[:,0,0] = position_offsetH
#pairs[:,0,1] = reward_high
pairs[:,0,1] = high_prob
pairs[:,0,2] = location_int
pairs[:,1,0] = position_offsetL
#pairs[:,1,1] = reward_low
pairs[:,1,1] = low_prob
pairs[:,1,2] = 1 - location_int
return pairs
@staticmethod
def block_probabilistic_reward(length=1000, boundaries=(-18,18,-10,10,-15,15),reward_high_prob=80,reward_low_prob=40):
pairs = colored_targets_with_probabilistic_reward(length=length, boundaries=boundaries,reward_high_prob=reward_high_prob,reward_low_prob=reward_low_prob)
return pairs
@staticmethod
def colored_targets_with_randomwalk_reward(length=1000,reward_high_prob=80,reward_low_prob=40,reward_high_span = 20, reward_low_span = 20,step_size_mean = 0, step_size_var = 1):
"""
Generator should return array of ntrials x 2 x 3. The second dimension is for each target.
For example, first is the target with high probability of reward, and the second
entry is for the target with low probability of reward. The third dimension holds three variables indicating
position offset (yes/no), reward probability, and location (binary returned where the
ouput indicates either left or right). The variables reward_high_span and reward_low_span indicate the width
of the range that the high or low reward probability are allowed to span respectively, e.g. if reward_high_prob
is 80 and reward_high_span is 20, then the reward probability for the high value target will be bounded
between 60 and 100 percent.
"""
position_offsetH = np.random.randint(2,size=(1,length))
position_offsetL = np.random.randint(2,size=(1,length))
location_int = np.random.randint(2,size=(1,length))
# define variables for increments: amount of increment and in which direction (i.e. increasing or decreasing)
assign_rewardH = np.random.randn(1,length)
assign_rewardL = np.random.randn(1,length)
assign_rewardH_direction = np.random.randn(1,length)
assign_rewardL_direction = np.random.randn(1,length)
r_0_high = reward_high_prob
r_0_low = reward_low_prob
r_lowerbound_high = r_0_high - (reward_high_span/2)
r_upperbound_high = r_0_high + (reward_high_span/2)
r_lowerbound_low = r_0_low - (reward_low_span/2)
r_upperbound_low = r_0_low + (reward_low_span/2)
reward_high = np.zeros(length)
reward_low = np.zeros(length)
reward_high[0] = r_0_high
reward_low[0] = r_0_low
eps_high = assign_rewardH*step_size_mean + [2*(assign_rewardH_direction > 0) - 1]*step_size_var
eps_low = assign_rewardL*step_size_mean + [2*(assign_rewardL_direction > 0) - 1]*step_size_var
eps_high = eps_high.ravel()
eps_low = eps_low.ravel()
for i in range(1,length):
'''
assign_rewardH_direction = np.random.randn(1)
assign_rewardL_direction = np.random.randn(1)
assign_rewardH = np.random.randn(1)
if assign_rewardH_direction[i-1,] < 0:
eps_high = step_size_mean*assign_rewardH[i-1] - step_size_var
else:
eps_high = step_size_mean*assign_rewardH[i-1] + step_size_var
if assign_rewardL_direction[i] < 0:
eps_low = step_size_mean*assign_rewardL[i] - step_size_var
else:
eps_low = step_size_mean*assign_rewardL[i] + step_size_var
'''
reward_high[i] = reward_high[i-1] + eps_high[i-1]
reward_low[i] = reward_low[i-1] + eps_low[i-1]
reward_high[i] = (r_lowerbound_high < reward_high[i] < r_upperbound_high)*reward_high[i] + (r_lowerbound_high > reward_high[i])*(r_lowerbound_high+ eps_high[i-1]) + (r_upperbound_high < reward_high[i])*(r_upperbound_high - eps_high[i-1])
reward_low[i] = (r_lowerbound_low < reward_low[i] < r_upperbound_low)*reward_low[i] + (r_lowerbound_low > reward_low[i])*(r_lowerbound_low+ eps_low[i-1]) + (r_upperbound_low < reward_low[i])*(r_upperbound_low - eps_low[i-1])
pairs = np.zeros([length,2,3])
pairs[:,0,0] = position_offsetH
pairs[:,0,1] = reward_high
pairs[:,0,2] = location_int
pairs[:,1,0] = position_offsetL
pairs[:,1,1] = reward_low
pairs[:,1,2] = 1 - location_int
return pairs
@staticmethod
def randomwalk_probabilistic_reward(length=1000,reward_high_prob=80,reward_low_prob=40,reward_high_span = 20, reward_low_span = 20,step_size_mean = 0, step_size_var = 1):
pairs = colored_targets_with_randomwalk_reward(length=length,reward_high_prob=reward_high_prob,reward_low_prob=reward_low_prob,reward_high_span = reward_high_span, reward_low_span = reward_low_span,step_size_mean = step_size_mean, step_size_var = step_size_var)
return pairs
def __init__(self, *args, **kwargs):
# Initialize the dynamics world
# world = ode.World() # TODO this should be part of the window, for object collision detection stuff
# world.setGravity((0,0,0))
# Arm link lengths----from monkey P? Numbers taken from MATLAB code originally written by Rodolphe Heliot/Amy Orsborn
# Changed to these values because most common among old code. Cheng & Scott 2000 Table 2 has other values if change needed
self.l_ua = 0.01 * 17.70 # m
self.l_fa = 0.01 * 20.35 # m
# Friction coefficients
self.B = np.mat([[0.03, 0.01],
[0.01, 0.03]])
# Mass of upperarm/forearm from Cheng & Scott, 2000, p221, Table 8 (based on morphometric data)
self.m_ua = 0.001*(23 + 34.4*body_weight) # kg (regression data specified in grams)
self.m_fa = 0.001*(53 + 25.2*body_weight) # kg
## Determine the inertia of each segment
rad_of_gyration = np.array([0.247, 0.248]) # relative to the length of each segment
# Calculate center of mass for each segment
self.r_ua = self.ctr_of_mass_ua = self.l_ua * rad_of_gyration[0]
self.r_fa = self.ctr_of_mass_fa = self.l_fa * rad_of_gyration[1]
# Calculate moment of inertia for each segment
# i = 0.001 * 0.0001 * (b + m*total_body_weight), where 'b' and 'm' are from Cheng & Scott 2000, p221, Table 8
# 0.001 * 0.0001 converts (g cm^2) ==> (kg m^2)
self.I_ua = 0.001*0.0001*(432 + 356.6*body_weight)
self.I_fa = 0.001*0.0001*(2381 + 861.6*body_weight)
self.num_joints = 2
self.theta = np.zeros(2) # angular
self.omega = np.zeros(2) # angular vel
self.alpha = np.zeros(2) # angular acc
self.torque = np.zeros(2)
base_loc = np.array([2., 0., -15])
self.base_loc = base_loc
link_radii=arm_radius
joint_radii=arm_radius
joint_colors=arm_color
link_colors=arm_color
self.link_lengths = link_lengths = np.array([self.l_ua, self.l_fa])
self.curr_vecs = np.zeros([self.num_joints, 3]) #rows go from proximal to distal links
self.chain = Chain(link_radii, joint_radii, list(link_lengths * 100), joint_colors, link_colors)
self.cursor = Sphere(radius=arm_radius/2, color=link_colors)
self.graphics_models = [self.chain.link_groups[0], self.cursor]
self.chain.translate(*self.base_loc, reset=True)
self.kin_chain = robot_arms.PlanarXZKinematicChain2Link(link_lengths * 100, base_loc=base_loc) # Multiplying by 100 to convert from m to cm
self.stay_on_screen = False
self.visible = True
self.n_muscles = len(muscles)
self.muscle_vel = np.zeros(self.n_muscles)
self.call_count = 0
class ActiveExoPlant(plants.Plant):
n_joints = 5
force_sensor_offset = 1544.
def __init__(self, *args, **kwargs):
if SIM:
self.rx_port = ('localhost', 60000)
self.tx_port = ('localhost', 60001)
else:
self.rx_port = ('10.0.0.1', 60000)
self.tx_port = ('10.0.0.14', 60001)
self.has_force_sensor = kwargs.pop('has_force_sensor', True)
self.hdf_attrs = [('joint_angles', 'f8', (5,)), ('joint_velocities', 'f8', (5,)), ('joint_applied_torque', 'f8', (5,)),]
if self.has_force_sensor and not ('endpt_force' in self.hdf_attrs):
self.hdf_attrs.append(('endpt_force', 'f8', (1,)))
# Initialize sockets for transmitting velocity commands / receiving sensor data
tx_sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
self.tx_sock = tx_sock
## kinematic chain
self.kin_chain = ActiveExoChain()
# joint limits in radians, based on mechanical limits---some configurations
# may still be outside the comfortable range for the subject
self.kin_chain.joint_limits = [(-1.25, 1.25), (0, 1.7), (-0.95, 0.9), (0, 1.4), (-1.5, 1.5)]
## Graphics, for experimenter only
self.link_lengths = link_lengths
self.cursor = Sphere(radius=arm_radius/2, color=arm_color)
self.upperarm_graphics = Cylinder(radius=arm_radius, height=self.link_lengths[0], color=arm_color)
# self.upperarm_graphics.xfm.translate(*exo_chain_graphics_base_loc)
self.forearm_graphics = Cone(radius1=arm_radius, radius2=arm_radius/3, height=self.link_lengths[1], color=arm_color)
self.forearm_graphics.xfm.translate(*exo_chain_graphics_base_loc)
self.graphics_models = [self.upperarm_graphics, self.forearm_graphics, self.cursor]
self.enabled = True
super(ActiveExoPlant, self).__init__(*args, **kwargs)
def disable(self):
self.enabled = False
def enable(self):
self.enabled = True
def start(self):
self.rx_sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
self.rx_sock.bind(self.rx_port)
super(ActiveExoPlant, self).start()
def _get_sensor_data(self):
if not hasattr(self, 'rx_sock'):
raise Exception("You seem to have forgotten to 'start' the plant!")
tx_sock, rx_sock = self.tx_sock, self.rx_sock
tx_sock.sendto('s', self.tx_port)
self._read_sock()
def _check_if_ready(self):
tx_sock, rx_sock = self.tx_sock, self.rx_sock
socket_list = [self.rx_sock]
tx_sock.sendto('s', self.tx_port)
time.sleep(0.5)
# Get the list sockets which are readable
read_sockets, write_sockets, error_sockets = select.select(socket_list , [], [], 0)
return self.rx_sock in read_sockets
def _read_sock(self):
n_header_bytes = 4
n_bytes_per_int = 2
n_rx_bytes = n_header_bytes*3 + 3*self.n_joints*n_bytes_per_double
fmt = '>IdddddIdddddIddddd'
if self.has_force_sensor:
n_rx_bytes += n_bytes_per_int
fmt += 'H'
bin_data = self.rx_sock.recvfrom(n_rx_bytes)
data = np.array(struct.unpack(fmt, bin_data[0]))
if self.has_force_sensor:
force_adc_data = data[-1]
frac_of_max_force = (force_adc_data - self.force_sensor_offset)/(2**14 - self.force_sensor_offset)
force_lbs = frac_of_max_force * 10
force_N = force_lbs * 4.448221628254617
self.force_N = max(force_N, 0) # force must be positive for this sensor
data = data[:-1]
data = data.reshape(3, self.n_joints + 1)
data = data[:,1:]
self.joint_angles, self.joint_velocities, self.joint_applied_torque = data
def get_data_to_save(self):
if not hasattr(self, 'joint_angles'):
print "No data has been acquired yet!"
return dict()
data = dict(joint_angles=self.joint_angles, joint_velocities=self.joint_velocities, joint_applied_torque=self.joint_applied_torque)
if self.has_force_sensor:
data['endpt_force'] = self.force_N
return data
def _set_joint_velocity(self, vel):
if not len(vel) == self.n_joints:
raise ValueError("Improper number of joint velocities!")
if self.enabled:
vel = vel.ravel()
else:
vel = np.zeros(5)
self.tx_sock.sendto(struct.pack('>I' + 'd'*self.n_joints, self.n_joints, vel[0], vel[1], vel[2], vel[3], vel[4]), self.tx_port)
self._read_sock()
def stop_vel(self):
self._set_joint_velocity(np.zeros(5))
def stop(self):
self.rx_sock.close()
print "RX socket closed!"
def set_intrinsic_coordinates(self, theta):
'''
Set the joint by specifying the angle in radians. Theta is a list of angles. If an element of theta = NaN, angle should remain the same.
'''
joint_locations = self.kin_chain.spatial_positions_of_joints(theta)
vec_sh_to_elbow = joint_locations[:,2]
vec_elbow_to_endpt = joint_locations[:,4] - joint_locations[:,2]
self.upperarm_graphics.xfm.rotate = Quaternion.rotate_vecs((0,0,1), vec_sh_to_elbow)
# self.upperarm_graphics.xfm.translate(*exo_chain_graphics_base_loc)
self.forearm_graphics.xfm.rotate = Quaternion.rotate_vecs((0,0,1), vec_elbow_to_endpt)
self.forearm_graphics.xfm.translate(*vec_sh_to_elbow, reset=True)
self.upperarm_graphics._recache_xfm()
self.forearm_graphics._recache_xfm()
self.cursor.translate(*self.get_endpoint_pos(), reset=True)
def get_intrinsic_coordinates(self, new=False):
if new or not hasattr(self, 'joint_angles'):
self._get_sensor_data()
return self.joint_angles
def get_endpoint_pos(self):
if not hasattr(self, 'joint_angles'):
self._get_sensor_data()
return self.kin_chain.endpoint_pos(self.joint_angles)
def draw_state(self):
self._get_sensor_data()
self.set_intrinsic_coordinates(self.joint_angles)
def drive(self, decoder):
# import pdb; pdb.set_trace()
joint_vel = decoder['qdot']
joint_vel[joint_vel > 0.2] = 0.2
joint_vel[joint_vel < -0.2] = -0.2
joint_vel[np.abs(joint_vel) < 0.02] = 0
# send the command to the robot
self._set_joint_velocity(joint_vel)
# set the decoder state to the actual joint angles
decoder['q'] = self.joint_angles
self.set_intrinsic_coordinates(self.joint_angles)
def vel_control_to_joint_config(self, fb_ctrl, target_config, sim=True, control_rate=10, tol=np.deg2rad(10)):
'''
Parameters
----------
control_rate : int
Control rate, in Hz
'''
target_state = np.hstack([target_config, np.zeros_like(target_config), np.zeros_like(target_config), 1])
target_state = np.mat(target_state.reshape(-1,1))
if not sim:
self._get_sensor_data()
else:
# assume that self.joint_angles has been automagically set
pass
current_state = np.hstack([self.joint_angles, np.zeros_like(target_config), np.zeros_like(target_config), 1])
current_state = np.mat(current_state.reshape(-1,1))
N = 250
traj = np.zeros([current_state.shape[0], N]) * np.nan
for k in range(250):
print k
current_config = np.array(current_state[0:5, 0]).ravel()
# print current_config
if np.all(np.abs(current_config - target_config) < tol):
print np.abs(current_config - target_config)
print tol
break
current_state = fb_ctrl.calc_next_state(current_state, target_state)
traj[:,k] = np.array(current_state).ravel()
if sim:
pass
else:
current_vel = np.array(current_state[5:10,0]).ravel()
self._set_joint_velocity(current_vel)
# update the current state using the joint encoders
current_state = np.hstack([self.joint_angles, np.zeros_like(target_config), np.zeros_like(target_config), 1])
current_state = np.mat(current_state.reshape(-1,1))
time.sleep(1./control_rate)
return traj
class TestBoundary(Window):
'''
A very simple task that displays a marker at the specified screen locations.
Useful for determining reasonable boundary values for targets.
'''
status = dict(wait=dict(stop=None))
state = "wait"
boundaries = traits.Tuple((-18, 18, -10, 10, -12, 12),
desc="x,y,z boundaries to display")
def __init__(self, **kwargs):
super(TestBoundary, self).__init__(**kwargs)
# Create a small sphere for each of the 6 boundary marks
self.xmin = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.xmin)
self.xmax = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.xmax)
self.ymin = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.ymin)
self.ymax = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.ymax)
self.zmin = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.zmin)
self.zmax = Sphere(radius=.1, color=(.5, 0, .5, 1))
self.add_model(self.zmax)
def _start_wait(self):
self.xmin.translate(self.boundaries[0], 0, 0, reset=True)
self.xmin.attach()
self.xmax.translate(self.boundaries[1], 0, 0, reset=True)
self.xmax.attach()
self.ymin.translate(0, self.boundaries[2], 0, reset=True)
self.ymin.attach()
self.ymax.translate(0, self.boundaries[3], 0, reset=True)
self.ymax.attach()
self.zmin.translate(0, 0, self.boundaries[4], reset=True)
self.zmin.attach()
self.zmax.translate(0, 0, self.boundaries[5], reset=True)
self.zmax.attach()
self.requeue()
def _while_wait(self):
self.draw_world()
def __init__(self, **kwargs):
super(FixationTraining, self).__init__(**kwargs)
self.fixation_point = Sphere(radius=.1, color=(1, 0, 0, 1))