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Maya-Mocap viz tools and added items to to-do list

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README.md
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@ -44,9 +44,9 @@ To upgrade, type `pip install pose2sim --upgrade`. You will need to update your
2. [Calculate from scratch](#calculate-from-scratch) 2. [Calculate from scratch](#calculate-from-scratch)
4. [Camera synchronization](#camera-synchronization) 4. [Camera synchronization](#camera-synchronization)
5. [Tracking, Triangulating, Filtering](#tracking-triangulating-filtering) 5. [Tracking, Triangulating, Filtering](#tracking-triangulating-filtering)
1. [Tracking the person of interest](#tracking-the-person-of-interest) 1. [Associate persons across cameras](#associate-persons-across-cameras)
2. [Triangulating keypoints](#triangulating-keypoints) 2. [Triangulating keypoints](#triangulating-keypoints)
3. [Filtering 3D coordinates](#filtering-3D-coordinates) 3. [Filtering 3D coordinates](#filtering-3d-coordinates)
6. [OpenSim kinematics](#opensim-kinematics) 6. [OpenSim kinematics](#opensim-kinematics)
3. [Utilities](#utilities) 3. [Utilities](#utilities)
4. [How to cite and how to contribute](#how-to-cite-and-how-to-contribute) 4. [How to cite and how to contribute](#how-to-cite-and-how-to-contribute)
@ -233,7 +233,8 @@ N.B.: Markers are not needed in Pose2Sim and were used here for validation
</details> </details>
## Camera calibration ## Camera calibration
> _**Convert a preexisting calibration file, or calculate intrinsic and extrinsic parameters from scratch.**_ > _**Convert a preexisting calibration file, or calculate intrinsic and extrinsic parameters from scratch.**_ \
> _**N.B.:**_ You can visualize your resulting camera calibration with my (experimental) [Maya-Mocap tool](https://github.com/davidpagnon/Maya-Mocap).
### Convert from Qualisys, Optitrack, or Vicon ### Convert from Qualisys, Optitrack, or Vicon
@ -414,7 +415,8 @@ Output:\
### Triangulating keypoints ### Triangulating keypoints
> _**Triangulate your 2D coordinates in a robust way.**_ > _**Triangulate your 2D coordinates in a robust way.**_ \
> _**N.B.:**_ You can visualize your resulting 3D coordinates with my (experimental) [Maya-Mocap tool](https://github.com/davidpagnon/Maya-Mocap).
Open an Anaconda prompt or a terminal, type `ipython`.\ Open an Anaconda prompt or a terminal, type `ipython`.\
By default, `triangulation()` will look for `Config.toml` in the `User` folder of your current directory. If you want to store it somewhere else (e.g. in your data directory), specify this path as an argument: `Pose2Sim.triangulation(r'path_to_config.toml')`. By default, `triangulation()` will look for `Config.toml` in the `User` folder of your current directory. If you want to store it somewhere else (e.g. in your data directory), specify this path as an argument: `Pose2Sim.triangulation(r'path_to_config.toml')`.
@ -478,7 +480,8 @@ Output:\
### Filtering 3D coordinates ### Filtering 3D coordinates
> _**Filter your 3D coordinates.**_ > _**Filter your 3D coordinates.**_\
> _**N.B.:**_ You can visualize your resulting filtered 3D coordinates with my (experimental) [Maya-Mocap tool](https://github.com/davidpagnon/Maya-Mocap).
Open an Anaconda prompt or a terminal, type `ipython`.\ Open an Anaconda prompt or a terminal, type `ipython`.\
By default, `filtering()` will look for `Config.toml` in the `User` folder of your current directory. If you want to store it somewhere else (e.g. in your data directory), specify this path as an argument: `Pose2Sim.filtering(r'path_to_config.toml')`. By default, `filtering()` will look for `Config.toml` in the `User` folder of your current directory. If you want to store it somewhere else (e.g. in your data directory), specify this path as an argument: `Pose2Sim.filtering(r'path_to_config.toml')`.
@ -779,10 +782,11 @@ If you want to contribute to Pose2Sim, please follow [this guide](https://docs.g
</br> </br>
> - [x] **Triangulation:** Triangulation weighted with confidence. > - [x] **Triangulation:** Triangulation weighted with confidence.
> - [x] **Triangulation:** Set likelihood threshold below which a camera should not be used, reprojection error threshold, and set minimum number of cameras allowed for triangulating a point. > - [x] **Triangulation:** Set a likelihood threshold below which a camera should not be used, a reprojection error threshold, and a minimum number of remaining cameras below which triangulation is skipped for this frame.
> - [x] **Triangulation:** Show mean reprojection error in px and in mm for each point. > - [x] **Triangulation:** Show mean reprojection error in px and in mm for each keypoint.
> - [x] **Triangulation:** Show how many cameras on average had to be excluded for each keypoint.
> - [x] **Triangulation:** Evaluate which cameras were the least reliable. > - [x] **Triangulation:** Evaluate which cameras were the least reliable.
> - [x] **Triangulation:** Show which frames had to be interpolated for each point. > - [x] **Triangulation:** Show which frames had to be interpolated for each keypoint.
> - [ ] **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). > - [ ] **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).
> - [ ] **Triangulation:** Multiple person kinematics (output multiple .trc coordinates files). > - [ ] **Triangulation:** Multiple person kinematics (output multiple .trc coordinates files).
> - [ ] **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)). > - [ ] **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)).
@ -818,4 +822,4 @@ If you want to contribute to Pose2Sim, please follow [this guide](https://docs.g
> - [ ] **Catch errors** > - [ ] **Catch errors**
> - [ ] **Conda package and Docker image** > - [ ] **Conda package and Docker image**
> - [ ] **Run from command line via click or typer** > - [ ] **Run from command line via click or typer**