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Merge branch 'main' of https://github.com/perfanalytics/pose2sim

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davidpagnon 2024-05-13 11:27:56 +02:00
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README.md
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@ -73,7 +73,7 @@ If you can only use one single camera and don't mind losing some accuracy, pleas
4. [Camera calibration](#camera-calibration) 4. [Camera calibration](#camera-calibration)
1. [Convert from Qualisys, Optitrack, Vicon, OpenCap, EasyMocap, or bioCV](#convert-from-qualisys-optitrack-vicon-opencap-easymocap-or-biocv) 1. [Convert from Qualisys, Optitrack, Vicon, OpenCap, EasyMocap, or bioCV](#convert-from-qualisys-optitrack-vicon-opencap-easymocap-or-biocv)
2. [Calculate from scratch](#calculate-from-scratch) 2. [Calculate from scratch](#calculate-from-scratch)
5. [Synchronization, Tracking, Triangulating, Filtering](#synchronization-tracking-triangulating-filtering) 5. [Synchronizing, Tracking, Triangulating, Filtering](#synchronizing-tracking-triangulating-filtering)
1. [Synchronization](#synchronization) 1. [Synchronization](#synchronization)
2. [Associate persons across cameras](#associate-persons-across-cameras) 2. [Associate persons across cameras](#associate-persons-across-cameras)
3. [Triangulating keypoints](#triangulating-keypoints) 3. [Triangulating keypoints](#triangulating-keypoints)
@ -96,7 +96,7 @@ If you can only use one single camera and don't mind losing some accuracy, pleas
1. **Install OpenPose** (instructions [there](https://github.com/CMU-Perceptual-Computing-Lab/openpose/blob/master/doc/installation/0_index.md)). \ 1. **Install OpenPose** (instructions [there](https://github.com/CMU-Perceptual-Computing-Lab/openpose/blob/master/doc/installation/0_index.md)). \
*Windows portable demo is enough.* *Windows portable demo is enough.*
2. **Install OpenSim 4.x** ([there](https://simtk.org/frs/index.php?group_id=91)). \ 2. **Install OpenSim 4.x** ([there](https://simtk.org/frs/index.php?group_id=91)). \
*Tested up to v4.4-beta on Windows. Has to be compiled from source on Linux (see [there](https://simtk-confluence.stanford.edu:8443/display/OpenSim/Linux+Support)).* *Tested up to v4.5 on Windows. Has to be compiled from source on Linux (see [there](https://simtk-confluence.stanford.edu:8443/display/OpenSim/Linux+Support)).*
3. ***Optional.*** *Install Anaconda or [Miniconda](https://docs.conda.io/en/latest/miniconda.html). \ 3. ***Optional.*** *Install Anaconda or [Miniconda](https://docs.conda.io/en/latest/miniconda.html). \
Open an Anaconda terminal and create a virtual environment with typing:* Open an Anaconda terminal and create a virtual environment with typing:*
<pre><i>conda create -n Pose2Sim python=3.8 -y <pre><i>conda create -n Pose2Sim python=3.8 -y
@ -136,8 +136,11 @@ Pose2Sim.markerAugmentation()
``` ```
3D results are stored as .trc files in each trial folder in the `pose-3d` directory. 3D results are stored as .trc files in each trial folder in the `pose-3d` directory.
*N.B.:* Default parameters have been provided in [Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/S01_Demo_SingleTrial/Config.toml) but can be edited.\ *N.B.:* Default parameters have been provided in [Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/S01_Demo_SingleTrial/Config.toml) but can be edited.
*N.B.:* *Try the calibration tool by changing `calibration_type` to `calculate` instead of `convert` (more info [there](#calculate-from-scratch)).*
</br>
__*Go further:*__ Try the calibration tool by changing `calibration_type` to `calculate` instead of `convert` in [Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/S01_Demo_SingleTrial/Config.toml) (more info [there](#calculate-from-scratch)).
<br/> <br/>
@ -153,7 +156,7 @@ Pose2Sim.markerAugmentation()
### Inverse kinematics ### Inverse kinematics
1. Load the provided `IK_Setup_Pose2Sim_LSTM.xml` scaling file from `Pose2Sim/OpenSim_Setup`. *(Tools -> Inverse kinematics -> Load)* 1. Load the provided `IK_Setup_Pose2Sim_LSTM.xml` scaling file from `Pose2Sim/OpenSim_Setup`. *(Tools -> Inverse kinematics -> Load)*
2. Run. You should see your skeletal model move in the Vizualizer window. 2. Run. You should see your skeletal model move in the Visualizer window.
5. Your IK motion file will be saved in `S00_P00_OpenSim`. 5. Your IK motion file will be saved in `S00_P00_OpenSim`.
<br/> <br/>
@ -792,7 +795,6 @@ You will be proposed a to-do list, but please feel absolutely free to propose yo
&#10004; **Triangulation:** [Undistort](https://docs.opencv.org/3.4/da/d54/group__imgproc__transform.html#ga887960ea1bde84784e7f1710a922b93c) 2D points before triangulating (and [distort](https://github.com/lambdaloop/aniposelib/blob/d03b485c4e178d7cff076e9fe1ac36837db49158/aniposelib/cameras.py#L301) them before computing reprojection error). &#10004; **Triangulation:** [Undistort](https://docs.opencv.org/3.4/da/d54/group__imgproc__transform.html#ga887960ea1bde84784e7f1710a922b93c) 2D points before triangulating (and [distort](https://github.com/lambdaloop/aniposelib/blob/d03b485c4e178d7cff076e9fe1ac36837db49158/aniposelib/cameras.py#L301) them before computing reprojection error).
&#10004; **Triangulation:** Offer the possibility to augment the triangulated data with [the OpenCap LSTM](https://github.com/stanfordnmbl/opencap-core/blob/main/utilsAugmenter.py). Create "BODY_25_AUGMENTED" model, Scaling_setup, IK_Setup. &#10004; **Triangulation:** Offer the possibility to augment the triangulated data with [the OpenCap LSTM](https://github.com/stanfordnmbl/opencap-core/blob/main/utilsAugmenter.py). Create "BODY_25_AUGMENTED" model, Scaling_setup, IK_Setup.
&#10004; **Triangulation:** Multiple person kinematics (output multiple .trc coordinates files). Triangulate all persons with reprojection error above threshold, and identify them by minimizing their displacement across frames. &#10004; **Triangulation:** Multiple person kinematics (output multiple .trc coordinates files). Triangulate all persons with reprojection error above threshold, and identify them by minimizing their displacement across frames.
&#9634; **Triangulation:** If the gap is larger than the interpolation threshold, fill it with previous frames instead of leaving it blank.
&#9634; **Triangulation:** Pre-compile weighted_triangulation and reprojection with @jit(nopython=True, parallel=True) for faster execution. &#9634; **Triangulation:** Pre-compile weighted_triangulation and reprojection with @jit(nopython=True, parallel=True) for faster execution.
&#9634; **Triangulation:** Offer the possibility of triangulating with Sparse Bundle Adjustment (SBA), Extended Kalman Filter (EKF), Full Trajectory Estimation (FTE) (see [AcinoSet](https://github.com/African-Robotics-Unit/AcinoSet)). &#9634; **Triangulation:** Offer the possibility of triangulating with Sparse Bundle Adjustment (SBA), Extended Kalman Filter (EKF), Full Trajectory Estimation (FTE) (see [AcinoSet](https://github.com/African-Robotics-Unit/AcinoSet)).
&#9634; **Triangulation:** Implement normalized DLT and RANSAC triangulation, Outlier rejection (sliding z-score?), as well as a [triangulation refinement step](https://doi.org/10.1109/TMM.2022.3171102). &#9634; **Triangulation:** Implement normalized DLT and RANSAC triangulation, Outlier rejection (sliding z-score?), as well as a [triangulation refinement step](https://doi.org/10.1109/TMM.2022.3171102).

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setup.cfg
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@ -1,6 +1,6 @@
[metadata] [metadata]
name = pose2sim name = pose2sim
version = 0.8.1 version = 0.8.3
author = David Pagnon author = David Pagnon
author_email = contact@david-pagnon.com author_email = contact@david-pagnon.com
description = Perform a markerless kinematic analysis from multiple calibrated views as a unified workflow from an OpenPose input to an OpenSim result. description = Perform a markerless kinematic analysis from multiple calibrated views as a unified workflow from an OpenPose input to an OpenSim result.