fullproof until limb swapping solved
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davidpagnon
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@ -134,7 +134,7 @@ interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none
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# 'none' if you don't want to interpolate missing points
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interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -135,7 +135,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -135,7 +135,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -135,7 +135,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -134,7 +134,7 @@ interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none
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# 'none' if you don't want to interpolate missing points
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interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -135,7 +135,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -134,7 +134,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -134,7 +134,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -134,7 +134,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -135,7 +135,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -135,7 +135,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -135,7 +135,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -135,7 +135,7 @@
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## 'none' if you don't want to interpolate missing points
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# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
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# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
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# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
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# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
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# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
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@ -15,6 +15,9 @@
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Transforms from OpenSim's yup to Blender's zup unless you set direction = 'yup'
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Beware, it can be quite slow depending on the ccomplexity
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of the model and on the number of frames.
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Usage:
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from Pose2Sim.Utilities import bodykin_from_mot_osim; bodykin_from_mot_osim.bodykin_from_mot_osim_func(r'<input_mot_file>', r'<output_osim_file>', r'<output_csv_file>')
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python -m bodykin_from_mot_osim -m input_mot_file -o input_osim_file
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@ -75,10 +78,23 @@ def bodykin_from_mot_osim_func(*args):
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model = osim.Model(osim_path)
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motion_data = osim.TimeSeriesTable(motion_path)
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# # Degrees or radians
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# with open(motion_path) as m_p:
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# while True:
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# line = m_p.readline()
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# if 'inDegrees' in line:
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# break
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# if 'yes' in line:
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# in_degrees = True
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# else:
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# in_degrees = False
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# Model: get model coordinates and bodies
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model_coordSet = model.getCoordinateSet()
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coordinates = [model_coordSet.get(i) for i in range(model_coordSet.getSize())]
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coordinateNames = [c.getName() for c in coordinates]
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# coordinates = [model_coordSet.get(i) for i in range(model_coordSet.getSize())]
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# coordinates = [c for c in coordinates if '_beta' not in c.getName()]
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# coordinateNames = [c.getName() for c in coordinates]
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coordinateNames = motion_data.getColumnLabels()
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model_bodySet = model.getBodySet()
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bodies = [model_bodySet.get(i) for i in range(model_bodySet.getSize())]
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bodyNames = [b.getName() for b in bodies]
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@ -86,16 +102,21 @@ def bodykin_from_mot_osim_func(*args):
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# Motion: read coordinates and convert to radians
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times = motion_data.getIndependentColumn()
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motion_data_np = motion_data.getMatrix().to_numpy()
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for i in range(len(coordinates)):
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if coordinates[i].getMotionType() == 1: # 1: rotation, 2: translation, 3: coupled
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motion_data_np[:,i] = motion_data_np[:,i] * np.pi/180 # if rotation, convert to radians
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for i, c in enumerate(coordinateNames):
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if model_coordSet.get(c).getMotionType() == 1: # 1: rotation, 2: translation, 3: coupled
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if motion_data.getTableMetaDataAsString('inDegrees') == 'yes':
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# if in_degrees:
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# for i in range(len(coordinates)):
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# if coordinates[i].getMotionType() == 1: # 1: rotation, 2: translation, 3: coupled
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motion_data_np[:,i] = motion_data_np[:,i] * np.pi/180 # if rotation, convert to radians
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# Animate model
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state = model.initSystem()
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loc_rot_frame_all = []
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H_zup = np.array([[1,0,0,0], [0,0,-1,0], [0,1,0,0], [0,0,0,1]])
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print('Time frame:')
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for n in range(motion_data.getNumRows()):
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print(times[n], 's')
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# Set model struct in each time state
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for c, coord in enumerate(coordinateNames):
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model.getCoordinateSet().get(coord).setValue(state, motion_data_np[n,c])
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@ -1 +0,0 @@
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@ -10,6 +10,9 @@
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Build a trc file which stores all real and virtual markers
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calculated from a .mot motion file and a .osim model file.
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Beware, it can be quite slow depending on the ccomplexity
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of the model and on the number of frames.
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Usage:
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from Pose2Sim.Utilities import trc_from_mot_osim; trc_from_mot_osim.trc_from_mot_osim_func(r'<input_mot_file>', r'<output_osim_file>', r'<output_trc_file>')
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python -m trc_from_mot_osim -m input_mot_file -o input_osim_file
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@ -37,7 +40,7 @@ __status__ = "Development"
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## FUNCTIONS
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def get_marker_positions(motion_data, model):
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def get_marker_positions(motion_data, model, in_degrees=True):
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'''
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Get dataframe of marker positions
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@ -63,10 +66,12 @@ def get_marker_positions(motion_data, model):
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# Get marker positions at each state
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state = model.initSystem()
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marker_positions = []
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print('Time frame:')
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for n,t in enumerate(times):
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print(t, 's')
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# put the model in the right position
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for coord in joint_angle_set_names:
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if not coord.endswith('_tx') and not coord.endswith('_ty') and not coord.endswith('_tz'):
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if in_degrees and not coord.endswith('_tx') and not coord.endswith('_ty') and not coord.endswith('_tz'):
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value = motion_data_pd.loc[n,coord]*np.pi/180
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else:
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value = motion_data_pd.loc[n,coord]
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@ -109,7 +114,19 @@ def trc_from_mot_osim_func(*args):
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# Create dataframe with marker positions
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model = osim.Model(osim_path)
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motion_data = osim.TimeSeriesTable(motion_path)
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marker_positions_pd = get_marker_positions(motion_data, model)
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# In degrees or radians
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with open(motion_path) as m_p:
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while True:
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line = m_p.readline()
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if 'inDegrees' in line:
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break
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if 'yes' in line:
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in_degrees = True
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else:
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in_degrees = False
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marker_positions_pd = get_marker_positions(motion_data, model, in_degrees=in_degrees)
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# Trc header
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times = motion_data.getIndependentColumn()
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