def check_acc_difference(self, x, R_cylinder=[]):
point_list, x_range, z_range = self.__get_plane_position()
for point in point_list:
simulated_marker = point[0]
segment_data = SegmentData(self.__subject_data,
self.__moved_segment)
walking_data_1_df = segment_data.get_segment_walking_1_data(
self.__speed)
test_index = x.index
R_standing_to_ground = segment_data.get_segment_R()
marker_cali_matrix = segment_data.get_marker_cali_matrix(
self.__speed)
virtual_marker, R_IMU_transform = Processor.get_virtual_marker(
simulated_marker, walking_data_1_df, marker_cali_matrix,
R_standing_to_ground)
# Processor.check_virtual_marker(virtual_marker, walking_data_1_df, self.__moved_segment) # for check
acc_IMU = Processor.get_acc(virtual_marker, R_IMU_transform)
# if it was simulated on cylinder, a rotation around the cylinder surface is necessary
if len(R_cylinder) != 0:
acc_IMU = np.matmul(R_cylinder, acc_IMU.T).T
changed_columns = []
for acc_name in ['_acc_x', '_acc_y', '_acc_z']:
column = self.__moved_segment + acc_name
changed_columns.append(column)
plt.plot(acc_IMU[:, 0])
plt.plot(x[changed_columns].as_matrix()[:, 0])
score = r2_score(acc_IMU[:, 0], x[changed_columns].as_matrix()[:,
0])
plt.title('pelvis, x += ' + str(point[1]) + ', z += ' +
str(point[2]) + ', score = ' + str(score))
plt.show()
def __modify_gyr_test(self,
simulated_marker,
x_train,
x_test,
R_cylinder=[]):
segment_data = SegmentData(self.__subject_data, self.__moved_segment)
walking_data_1_df = segment_data.get_segment_walking_1_data(
self.__speed)
train_index = x_train.index
test_index = x_test.index
R_standing_to_ground = segment_data.get_segment_R()
marker_cali_matrix = segment_data.get_marker_cali_matrix(self.__speed)
virtual_marker, R_IMU_transform = Processor.get_virtual_marker(
simulated_marker, walking_data_1_df, marker_cali_matrix,
R_standing_to_ground)
# Processor.check_virtual_marker(virtual_marker, walking_data_1_df, self.__moved_segment) # for check
gyr_IMU = Processor.get_gyr(walking_data_1_df, R_IMU_transform)
# if it was simulated on cylinder, a rotation around the cylinder surface is necessary
if len(R_cylinder) != 0:
gyr_IMU = np.matmul(R_cylinder, gyr_IMU.T).T
changed_columns = []
for gyr_name in ['_gyr_x', '_gyr_y', '_gyr_z']:
column = self.__moved_segment + gyr_name
changed_columns.append(column)
gyr_IMU_df = pd.DataFrame(gyr_IMU)
# x_test is just a quote of the original x_test, deep copy so that no warning will show up
x_train_changed = x_train.copy()
x_test_changed = x_test.copy()
x_train_changed[changed_columns] = gyr_IMU_df.loc[train_index]
x_test_changed[changed_columns] = gyr_IMU_df.loc[test_index]
return x_train_changed, x_test_changed
def __init__(self, segment, axis_name, iterable_object, diameter=None):
self.__segment = segment
self.__i_offset = 0
if axis_name not in ['x', 'y', 'z', 'theta', 'rotation']:
raise RuntimeError('Wrong axis name.')
offsets = []
if axis_name is 'x':
for item in iterable_object:
offset = Offset(self.__segment, x_offset=item /
1000) # change millimeter to meter
offsets.append(offset)
elif axis_name is 'y':
for item in iterable_object:
offset = Offset(self.__segment, y_offset=item /
1000) # change millimeter to meter
offsets.append(offset)
elif axis_name is 'z':
for item in iterable_object:
offset = Offset(self.__segment, z_offset=item / 1000)
offsets.append(offset)
elif axis_name is 'theta':
if not diameter:
raise RuntimeError('Missing the cylinder diameter.')
for item in iterable_object:
theta_radians = item * np.pi / 180 # change degree to radians
if segment in ['l_thigh', 'l_shank']:
x = diameter / 2 * (1 - np.cos(theta_radians))
R_cylinder = Processor.get_cylinder_surface_rotation(
theta_radians)
else:
x = -diameter / 2 * (1 - np.cos(theta_radians))
R_cylinder = Processor.get_cylinder_surface_rotation(
-theta_radians)
y = diameter / 2 * np.sin(theta_radians)
offset = Offset(self.__segment,
x_offset=x,
y_offset=y,
theta_offset=item,
R=R_cylinder)
offsets.append(offset)
elif axis_name is 'rotation':
for rotation_angle in iterable_object:
R = Offset.rotation_angle_to_R(rotation_angle)
offset = Offset(self.__segment,
rotation_angle=rotation_angle,
R=R)
offsets.append(offset)
self.__offsets = offsets
def __initialize_offset(segment, axis_name, item, diameter=None):
if axis_name not in ['x', 'y', 'z', 'theta']:
raise RuntimeError('Wrong axis name.')
if axis_name is 'x':
offset = Offset(segment,
x_offset=item / 1000) # change millimeter to meter
elif axis_name is 'y':
offset = Offset(segment,
y_offset=item / 1000) # change millimeter to meter
elif axis_name is 'z':
offset = Offset(segment, z_offset=item / 1000)
else:
if not diameter:
raise RuntimeError('Missing the cylinder diameter.')
theta_radians = item * np.pi / 180 # change degree to radians
R_cylinder = Processor.get_cylinder_surface_rotation(theta_radians)
x = diameter / 2 * (1 - np.cos(theta_radians))
y = diameter / 2 * np.sin(theta_radians)
offset = Offset(segment=segment,
x_offset=x,
y_offset=y,
theta_offset=item,
R=R_cylinder)
return offset
def get_xy(self):
speed = self.__speed
walking_data_1_df = self.__subject_data.get_walking_1_data(speed)
# for now we only use walking data 1
data_len = walking_data_1_df.shape[0]
# get x
if self.__gyr_data:
x = np.zeros([data_len, 48])
else:
x = np.zeros([data_len, 24])
i_segment = 0
for segment_name in SEGMENT_NAMES:
segment_data = SegmentData(self.__subject_data, segment_name)
segment_data_walking_1_df = segment_data.get_segment_walking_1_data(
speed)
center_marker = segment_data.get_center_point_mean(speed)
R_standing_to_ground = segment_data.get_segment_R()
marker_cali_matrix = segment_data.get_marker_cali_matrix(speed)
virtual_marker, R_IMU_transform = Processor.get_virtual_marker(
center_marker, segment_data_walking_1_df, marker_cali_matrix,
R_standing_to_ground)
# Processor.check_virtual_marker(virtual_marker, walking_data_1_df, segment_name) # for check
acc_IMU = Processor.get_acc(virtual_marker, R_IMU_transform)
x[:, 3 * i_segment:3 * (i_segment + 1)] = acc_IMU
if self.__gyr_data:
gyr_IMU = Processor.get_gyr(segment_data_walking_1_df,
R_IMU_transform)
x[:, 24 + 3 * i_segment:24 + 3 * (i_segment + 1)] = gyr_IMU
i_segment += 1
x = pd.DataFrame(x)
if self.__gyr_data:
x.columns = ALL_ACC_GYR_NAMES
else:
x.columns = ALL_ACC_NAMES
# get y
y = walking_data_1_df[self.__output_names]
return x, y
def __get_cylinder_position(self):
segment_data = SegmentData(self.__subject_data, self.__moved_segment)
center_point_mean = segment_data.get_center_point_mean(self.__speed)
# range are in millimeter
theta_range, z_range = XYGenerator.get_move_range(self.__moved_segment)
cylinder_diameter = self.__subject_data.get_cylinder_diameter(
self.__moved_segment)
point_list = []
for theta in theta_range:
for z in z_range:
theta_radians = theta * np.pi / 180 # change degree to radians
R_cylinder = Processor.get_cylinder_surface_rotation(
theta_radians)
x = cylinder_diameter / 2 * (1 - np.cos(theta_radians))
y = cylinder_diameter / 2 * np.sin(theta_radians)
point = center_point_mean + np.array(
[x, y, z]) / 1000 # change milliter to meter
point_list.append([point, theta, z, R_cylinder])
self.__axis_1_range, self.__axis_2_range = theta_range, z_range
return point_list, theta_range, z_range