def compare_csv(filename, kind):
"""Assert analogs's to_csv method."""
idx = [0, 1, 2, 3]
out = Path(".") / "temp.csv"
if kind == "markers":
header = 2
arr_ref, arr = Markers3d(), Markers3d()
else:
header = 3
arr_ref, arr = Analogs3d(), Analogs3d()
# read a csv
arr_ref = arr_ref.from_csv(filename,
first_row=5,
first_column=2,
header=header,
prefix=":",
idx=idx)
# write a csv
arr_ref.to_csv(out, header=False)
# read the generated csv
arr = arr.from_csv(out,
first_row=0,
first_column=0,
header=0,
prefix=":",
idx=idx)
out.unlink()
a = arr_ref[:, :, 1:100]
b = arr[:, :, 1:100]
np.testing.assert_equal(a.shape, b.shape)
np.testing.assert_almost_equal(a, b, decimal=1)
def transpose(self):
"""
Returns
-------
Rt_t : RotoTrans
Transposed RotoTrans matrix ([R.T -R.T*t],[0 0 0 1])
"""
# Create a matrix with the transposed rotation part
rt_t = RotoTrans(rt=np.ndarray((4, 4, self.get_num_frames())))
rt_t[0:3, 0:3, :] = np.transpose(self[0:3, 0:3, :], (1, 0, 2))
# Fill the last column and row with 0 and bottom corner with 1
rt_t[3, 0:3, :] = 0
rt_t[0:3, 3, :] = 0
rt_t[3, 3, :] = 1
# Transpose the translation part
t = Markers3d(
data=np.reshape(self[0:3, 3, :], (3, 1, self.get_num_frames())))
rt_t[0:3, 3, :] = t.rotate(-rt_t)[0:3, :].reshape(
(3, self.get_num_frames()))
# Return transposed matrix
return rt_t
def test_markers(idx, names, expected_shape, expected_values, extension):
"""Assert markers shape."""
if extension == "csv":
arr = Markers3d.from_csv(
MARKERS_CSV,
first_row=5,
first_column=2,
header=2,
prefix=":",
idx=idx,
names=names,
)
elif extension == "xlsx":
arr = Markers3d.from_excel(
MARKERS_XLSX,
sheet_name=0,
first_row=5,
first_column=2,
header=2,
prefix=":",
idx=idx,
names=names,
)
elif extension == "c3d":
arr = Markers3d.from_c3d(MARKERS_ANALOGS_C3D,
prefix=":",
idx=idx,
names=names)
else:
raise ValueError(
f'extension should be "csv", "c3d" or "xlsx". You provided {extension}'
)
# test shape
np.testing.assert_equal(arr.shape, expected_shape)
# test values
d = arr[:, 0, int(arr.shape[2] / 2)]
np.testing.assert_almost_equal(d, expected_values, decimal=2)
def __init__(self, parent,
markers_size=5, markers_color=(1, 1, 1), markers_opacity=1.0,
rt_size=25):
"""
Creates a model that will holds things to plot
Parameters
----------
parent
Parent of the Model window
markers_size : float
Size the markers should be drawn
markers_color : Tuple(int)
Color the markers should be drawn (1 is max brightness)
markers_opacity : float
Opacity of the markers (0.0 is completely transparent, 1.0 completely opaque)
rt_size : int
Length of the axes of the system of axes
"""
QtWidgets.QWidget.__init__(self, parent)
self.parent_window = parent
palette = QPalette()
palette.setColor(self.backgroundRole(), QColor(255, 255, 255))
self.setAutoFillBackground(True)
self.setPalette(palette)
self.markers = Markers3d()
self.markers_size = markers_size
self.markers_color = markers_color
self.markers_opacity = markers_opacity
self.markers_actors = list()
self.all_rt = RotoTransCollection()
self.n_rt = 0
self.rt_size = rt_size
self.rt_actors = list()
self.parent_window.should_reset_camera = True
self.all_meshes = MeshCollection()
self.mesh_actors = list()
def __init__(self,
parent,
markers_size=0.010,
markers_color=(1, 1, 1),
markers_opacity=1.0,
global_ref_frame_length=0.15,
global_ref_frame_width=5,
global_center_of_mass_size=0.0075,
global_center_of_mass_color=(0, 0, 0),
global_center_of_mass_opacity=1.0,
segments_center_of_mass_size=0.005,
segments_center_of_mass_color=(0, 0, 0),
segments_center_of_mass_opacity=1.0,
mesh_color=(0, 0, 0),
mesh_opacity=1.0,
muscle_color=(150 / 255, 15 / 255, 15 / 255),
muscle_opacity=1.0,
rt_length=0.1,
rt_width=2):
"""
Creates a model that will holds things to plot
Parameters
----------
parent
Parent of the Model window
markers_size : float
Size the markers should be drawn
markers_color : Tuple(int)
Color the markers should be drawn (1 is max brightness)
markers_opacity : float
Opacity of the markers (0.0 is completely transparent, 1.0 completely opaque)
rt_length : int
Length of the axes of the system of axes
"""
QtWidgets.QWidget.__init__(self, parent)
self.parent_window = parent
palette = QPalette()
palette.setColor(self.backgroundRole(), QColor(255, 255, 255))
self.setAutoFillBackground(True)
self.setPalette(palette)
self.markers = Markers3d()
self.markers_size = markers_size
self.markers_color = markers_color
self.markers_opacity = markers_opacity
self.markers_actors = list()
self.has_global_ref_frame = False
self.global_ref_frame_length = global_ref_frame_length
self.global_ref_frame_width = global_ref_frame_width
self.global_center_of_mass = Markers3d()
self.global_center_of_mass_size = global_center_of_mass_size
self.global_center_of_mass_color = global_center_of_mass_color
self.global_center_of_mass_opacity = global_center_of_mass_opacity
self.global_center_of_mass_actors = list()
self.segments_center_of_mass = Markers3d()
self.segments_center_of_mass_size = segments_center_of_mass_size
self.segments_center_of_mass_color = segments_center_of_mass_color
self.segments_center_of_mass_opacity = segments_center_of_mass_opacity
self.segments_center_of_mass_actors = list()
self.all_rt = RotoTransCollection()
self.n_rt = 0
self.rt_length = rt_length
self.rt_width = rt_width
self.rt_actors = list()
self.parent_window.should_reset_camera = True
self.all_meshes = MeshCollection()
self.mesh_color = mesh_color
self.mesh_opacity = mesh_opacity
self.mesh_actors = list()
self.all_muscles = MeshCollection()
self.muscle_color = muscle_color
self.muscle_opacity = muscle_opacity
self.muscle_actors = list()
def __init__(self,
model_path=None,
loaded_model=None,
show_meshes=True,
show_global_center_of_mass=True,
show_segments_center_of_mass=True,
show_global_ref_frame=True,
show_local_ref_frame=True,
show_markers=True,
markers_size=0.010,
show_muscles=True,
show_analyses_panel=True,
**kwargs):
"""
Class that easily shows a biorbd model
Args:
loaded_model: reference to a biorbd loaded model (if both loaded_model and model_path, load_model is selected
model_path: path of the model to load
"""
# Load and store the model
if loaded_model is not None:
if not isinstance(loaded_model, biorbd.Model):
raise TypeError(
"loaded_model should be of a biorbd.Model type")
self.model = loaded_model
elif model_path is not None:
self.model = biorbd.Model(model_path)
else:
raise ValueError("loaded_model or model_path must be provided")
# Create the plot
self.vtk_window = VtkWindow(background_color=(.5, .5, .5))
self.vtk_model = VtkModel(self.vtk_window,
markers_color=(0, 0, 1),
markers_size=markers_size)
self.is_executing = False
self.animation_warning_already_shown = False
# Set Z vertical
cam = self.vtk_window.ren.GetActiveCamera()
cam.SetFocalPoint(0, 0, 0)
cam.SetPosition(5, 0, 0)
cam.SetRoll(-90)
# Get the options
self.show_markers = show_markers
self.show_global_ref_frame = show_global_ref_frame
self.show_global_center_of_mass = show_global_center_of_mass
self.show_segments_center_of_mass = show_segments_center_of_mass
self.show_local_ref_frame = show_local_ref_frame
if self.model.nbMuscles() > 0:
self.show_muscles = show_muscles
else:
self.show_muscles = False
if sum([
len(i)
for i in self.model.meshPoints(np.zeros(self.model.nbQ()))
]) > 0:
self.show_meshes = show_meshes
else:
self.show_meshes = 0
# Create all the reference to the things to plot
self.nQ = self.model.nbQ()
self.Q = np.zeros(self.nQ)
self.markers = Markers3d(np.ndarray((3, self.model.nbMarkers(), 1)))
if self.show_markers:
self.Markers = InterfacesCollections.Markers(self.model)
self.global_center_of_mass = Markers3d(np.ndarray((3, 1, 1)))
if self.show_global_center_of_mass:
self.CoM = InterfacesCollections.CoM(self.model)
self.segments_center_of_mass = Markers3d(
np.ndarray((3, self.model.nbSegment(), 1)))
if self.show_segments_center_of_mass:
self.CoMbySegment = InterfacesCollections.CoMbySegment(self.model)
if self.show_meshes:
self.mesh = MeshCollection()
self.meshPointsInMatrix = InterfacesCollections.MeshPointsInMatrix(
self.model)
for i, vertices in enumerate(
self.meshPointsInMatrix.get_data(Q=self.Q,
compute_kin=False)):
triangles = np.ndarray((len(self.model.meshFaces()[i]), 3),
dtype="int32")
for k, patch in enumerate(self.model.meshFaces()[i]):
triangles[k, :] = patch.face()
self.mesh.append(Mesh(vertex=vertices, triangles=triangles.T))
self.model.updateMuscles(self.Q, True)
self.muscles = MeshCollection()
for group_idx in range(self.model.nbMuscleGroups()):
for muscle_idx in range(
self.model.muscleGroup(group_idx).nbMuscles()):
musc = self.model.muscleGroup(group_idx).muscle(muscle_idx)
tp = np.zeros(
(3, len(musc.position().musclesPointsInGlobal()), 1))
self.muscles.append(Mesh(vertex=tp))
self.musclesPointsInGlobal = InterfacesCollections.MusclesPointsInGlobal(
self.model)
self.rt = RotoTransCollection()
self.allGlobalJCS = InterfacesCollections.AllGlobalJCS(self.model)
for rt in self.allGlobalJCS.get_data(Q=self.Q, compute_kin=False):
self.rt.append(RotoTrans(rt))
if self.show_global_ref_frame:
self.vtk_model.create_global_ref_frame()
self.show_analyses_panel = show_analyses_panel
if self.show_analyses_panel:
self.muscle_analyses = []
self.palette_active = QPalette()
self.palette_inactive = QPalette()
self.set_viz_palette()
self.animated_Q = []
self.play_stop_push_button = []
self.is_animating = False
self.is_recording = False
self.start_icon = QIcon(
QPixmap(f"{os.path.dirname(__file__)}/ressources/start.png"))
self.pause_icon = QIcon(
QPixmap(f"{os.path.dirname(__file__)}/ressources/pause.png"))
self.record_icon = QIcon(
QPixmap(f"{os.path.dirname(__file__)}/ressources/record.png"))
self.add_icon = QIcon(
QPixmap(f"{os.path.dirname(__file__)}/ressources/add.png"))
self.stop_icon = QIcon(
QPixmap(f"{os.path.dirname(__file__)}/ressources/stop.png"))
self.double_factor = 10000
self.sliders = list()
self.movement_slider = []
self.active_analyses_widget = None
self.analyses_layout = QHBoxLayout()
self.analyses_muscle_widget = QWidget()
self.add_options_panel()
# Update everything at the position Q=0
self.set_q(self.Q)
def __init__(self,
model_path=None,
loaded_model=None,
show_global_ref_frame=True,
show_markers=True,
show_global_center_of_mass=True,
show_segments_center_of_mass=True,
show_rt=True,
show_muscles=True,
show_meshes=True,
show_options=True):
"""
Class that easily shows a biorbd model
Args:
loaded_model: reference to a biorbd loaded model (if both loaded_model and model_path, load_model is selected
model_path: path of the model to load
"""
# Load and store the model
if loaded_model is not None:
if not isinstance(loaded_model, biorbd.Model):
raise TypeError(
"loaded_model should be of a biorbd.Model type")
self.model = loaded_model
elif model_path is not None:
self.model = biorbd.Model(model_path)
else:
raise ValueError("loaded_model or model_path must be provided")
# Create the plot
self.vtk_window = VtkWindow(background_color=(.5, .5, .5))
self.vtk_model = VtkModel(self.vtk_window, markers_color=(0, 0, 1))
self.is_executing = False
self.animation_warning_already_shown = False
# Set Z vertical
cam = self.vtk_window.ren.GetActiveCamera()
cam.SetFocalPoint(0, 0, 0)
cam.SetPosition(5, 0, 0)
cam.SetRoll(-90)
# Get the options
self.show_markers = show_markers
self.show_global_ref_frame = show_global_ref_frame
self.show_global_center_of_mass = show_global_center_of_mass
self.show_segments_center_of_mass = show_segments_center_of_mass
self.show_rt = show_rt
if self.model.nbMuscleTotal() > 0:
self.show_muscles = show_muscles
else:
self.show_muscles = False
if sum([
len(i)
for i in self.model.meshPoints(np.zeros(self.model.nbQ()))
]) > 0:
self.show_meshes = show_meshes
else:
self.show_meshes = 0
# Create all the reference to the things to plot
self.nQ = self.model.nbQ()
self.Q = np.zeros(self.nQ)
self.markers = Markers3d(np.ndarray((3, self.model.nTags(), 1)))
self.global_center_of_mass = Markers3d(np.ndarray((3, 1, 1)))
self.segments_center_of_mass = Markers3d(
np.ndarray((3, self.model.nbBone(), 1)))
self.mesh = MeshCollection()
for l, meshes in enumerate(self.model.meshPoints(self.Q)):
tp = np.ndarray((3, len(meshes), 1))
for k, mesh in enumerate(meshes):
tp[:, k, 0] = mesh.get_array()
self.mesh.append(Mesh(vertex=tp))
self.model.updateMuscles(self.model, self.Q, True)
self.muscles = MeshCollection()
for group_idx in range(self.model.nbMuscleGroups()):
for muscle_idx in range(
self.model.muscleGroup(group_idx).nbMuscles()):
musc_tp = self.model.muscleGroup(group_idx).muscle(muscle_idx)
muscle_type = biorbd.Model.getMuscleType(musc_tp).getString()
if muscle_type == "Hill":
musc = biorbd.HillType(musc_tp)
elif muscle_type == "HillThelen":
musc = biorbd.HillTypeThelen(musc_tp)
elif muscle_type == "HillSimple":
musc = biorbd.HillTypeSimple(musc_tp)
tp = np.ndarray(
(3, len(musc.position().musclesPointsInGlobal()), 1))
for k, pts in enumerate(
musc.position().musclesPointsInGlobal()):
tp[:, k, 0] = pts.get_array()
self.muscles.append(Mesh(vertex=tp))
self.rt = RotoTransCollection()
for rt in self.model.globalJCS(self.Q):
self.rt.append(RotoTrans(rt.get_array()))
if self.show_global_ref_frame:
self.vtk_model.create_global_ref_frame()
self.show_options = show_options
if self.show_options:
self.muscle_analyses = []
self.palette_active = QPalette()
self.palette_inactive = QPalette()
self.set_viz_palette()
self.animated_Q = []
self.play_stop_push_button = []
self.is_animating = False
self.start_icon = QIcon(
QPixmap(f"{os.path.dirname(__file__)}/ressources/start.png"))
self.stop_icon = QIcon(
QPixmap(f"{os.path.dirname(__file__)}/ressources/pause.png"))
self.double_factor = 10000
self.sliders = list()
self.movement_slider = []
self.active_analyses_widget = None
self.analyses_layout = QHBoxLayout()
self.analyses_muscle_widget = QWidget()
self.add_options_panel()
# Update everything at the position Q=0
self.set_q(self.Q)
"""
Example script for file IO
"""
from pathlib import Path
from pyomeca import Markers3d, Analogs3d
# Path to data
DATA_FOLDER = Path('..') / 'tests' / 'data'
MARKERS_CSV = DATA_FOLDER / 'markers.csv'
MARKERS_ANALOGS_C3D = DATA_FOLDER / 'markers_analogs.c3d'
ANALOGS_CSV = DATA_FOLDER / 'analogs.csv'
# read 11 first markers of a csv file
markers_1 = Markers3d.from_csv(MARKERS_CSV, first_row=5, first_column=2, header=2,
idx=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], prefix=':')
# mean of 1st and 4th markers of a csv file
markers_2 = Markers3d.from_csv(MARKERS_CSV, first_row=5, first_column=2, header=2,
idx=[[0, 1, 2], [0, 4, 2]], prefix=':')
# get markers by names in a csv file
markers_3 = Markers3d.from_csv(MARKERS_CSV, first_row=5, first_column=2, header=2,
names=['CLAV_post', 'PSISl', 'STERr', 'CLAV_post'], prefix=':')
# write a csv file from a Markers3d types
markers_3.to_csv('../Misc/mtest.csv', header=False)
# read 4 first markers of a c3d file
markers_4 = Markers3d.from_c3d(MARKERS_ANALOGS_C3D, idx=[0, 1, 2, 3])
]
nTriPod = 6
nMarkOnInsole = 55
forceRetrainingModel = False
rtm = [
6, 7, 8
] # idx of the markers in training file of the Tripod at the back of the insole [left, top, right]
show_in_global = False
calculate_error = True
new_marker_tripod_names = False
show_animation = True
show_individual_plots = True
# load dataSet
dataSet = Markers3d.from_c3d(trainingFileName,
names=name_markers).low_pass(freq=100,
order=4,
cutoff=10)
# Get markers in a known reference frame
# rt = RotoTrans.define_axes(dataSet, [rtm[2], rtm[0]], [[rtm[0], rtm[1]], [rtm[2], rtm[1]]], "xz", "z", rtm)
rt = RotoTrans.define_axes(dataSet, [0, 4 * 3],
[[0, 5 * 3], [2 * 3 + 1, 2 * 3 + 1]], "xz", "z",
[0, 2 * 3 + 1, 5 * 3])
dataSet = dataSet.rotate(rt.transpose())
# split into input (X) and output (Y) variables
X = dataSet[:, 0:nTriPod * 3, :].to_2d()
Y = dataSet[:, nTriPod * 3:nTriPod * 3 + nMarkOnInsole, :].to_2d()
# X_train, X_test, y_train, y_test = train_test_split(X, Y, test_size=0.2, train_size=0.8)
X_train = X
y_train = Y
import numpy as np
from pyomeca import FrameDependentNpArray, Markers3d, RotoTrans, RotoTransCollection
from BiorbdViz.biorbd_vtk import VtkModel, VtkWindow, Mesh, MeshCollection
# Path to data
DATA_FOLDER = Path(
'/home/pariterre/Programmation/biorbd-viz') / 'tests' / 'data'
MARKERS_CSV = DATA_FOLDER / 'markers.csv'
MARKERS_ANALOGS_C3D = DATA_FOLDER / 'markers_analogs.c3d'
# Load data
# all markers
d = Markers3d.from_c3d(MARKERS_ANALOGS_C3D,
idx=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
prefix=':')
# mean of 1st and 4th
d2 = Markers3d.from_c3d(MARKERS_ANALOGS_C3D,
idx=[[0, 1, 2], [0, 4, 2]],
prefix=':')
# mean of first 3 markers
d3 = Markers3d.from_c3d(MARKERS_ANALOGS_C3D, idx=[[0], [1], [2]], prefix=':')
d4 = Markers3d.from_c3d(MARKERS_ANALOGS_C3D,
names=['CLAV_post', 'PSISl', 'STERr', 'CLAV_post'],
prefix=':')
# mean of first 3 markers in c3d file
d5 = Markers3d.from_c3d(MARKERS_ANALOGS_C3D, idx=[[0], [1], [2]], prefix=':')
from pathlib import Path
import numpy as np
from pyomeca import FrameDependentNpArray, Markers3d, RotoTrans, RotoTransCollection
from BiorbdViz.biorbd_vtk import VtkModel, VtkWindow, Mesh, MeshCollection
# Path to data
DATA_FOLDER = Path("/home/pariterre/Programmation/biorbd-viz") / "tests" / "data"
MARKERS_CSV = DATA_FOLDER / "markers.csv"
MARKERS_ANALOGS_C3D = DATA_FOLDER / "markers_analogs.c3d"
# Load data
# all markers
d = Markers3d.from_c3d(MARKERS_ANALOGS_C3D, idx=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], prefix=":")
# mean of 1st and 4th
d2 = Markers3d.from_c3d(MARKERS_ANALOGS_C3D, idx=[[0, 1, 2], [0, 4, 2]], prefix=":")
# mean of first 3 markers
d3 = Markers3d.from_c3d(MARKERS_ANALOGS_C3D, idx=[[0], [1], [2]], prefix=":")
d4 = Markers3d.from_c3d(MARKERS_ANALOGS_C3D, names=["CLAV_post", "PSISl", "STERr", "CLAV_post"], prefix=":")
# mean of first 3 markers in c3d file
d5 = Markers3d.from_c3d(MARKERS_ANALOGS_C3D, idx=[[0], [1], [2]], prefix=":")
# Create a windows with a nice gray background
vtkWindow = VtkWindow(background_color=(0.5, 0.5, 0.5))
# Add marker holders to the window
vtkModelReal = VtkModel(vtkWindow, markers_color=(1, 0, 0), markers_size=10.0, markers_opacity=1)
from pathlib import Path
from pyomeca import Markers3d, Analogs3d
# Path to data
DATA_FOLDER = Path("..") / "tests" / "data"
MARKERS_CSV = DATA_FOLDER / "markers.csv"
MARKERS_ANALOGS_C3D = DATA_FOLDER / "markers_analogs.c3d"
ANALOGS_CSV = DATA_FOLDER / "analogs.csv"
# read 11 first markers of a csv file
markers_1 = Markers3d.from_csv(
MARKERS_CSV,
first_row=5,
first_column=2,
header=2,
idx=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
prefix=":",
)
# mean of 1st and 4th markers of a csv file
markers_2 = Markers3d.from_csv(
MARKERS_CSV,
first_row=5,
first_column=2,
header=2,
idx=[[0, 1, 2], [0, 4, 2]],
prefix=":",
)
# get markers by names in a csv file