To upgrade, type `pip install pose2sim --upgrade`. You will need to update your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file.\
`Pose2Sim` provides a workflow for 3D markerless kinematics, as an alternative to the more usual marker-based motion capture methods.\
Pose2Sim stands for "OpenPose to OpenSim", as it uses OpenPose inputs (2D keypoints coordinates obtained from multiple videos) and leads to an OpenSim result (full-body 3D joint angles). Other 2D solutions can alternatively be used as inputs.
*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)).*
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:*
*N.B.:* Default parameters have been provided in [Demo\User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Demo/User/Config.toml) but can be edited.\
2. Edit the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file as needed, **especially regarding the path to your project**.
N.B.: Note that the names of your camera folders must follow the same order as in the calibration file, and end with '_json'.
### With OpenPose:
The accuracy and robustness of Pose2Sim have been thoroughly assessed only with OpenPose, and especially with the BODY_25B model. Consequently, we recommend using this 2D pose estimation solution. See [OpenPose repository](https://github.com/CMU-Perceptual-Computing-Lab/openpose) for installation and running.
* Open a command prompt in your **OpenPose** directory. \
* The [BODY_25B model](https://github.com/CMU-Perceptual-Computing-Lab/openpose_train/tree/master/experimental_models) has more accurate results than the standard BODY_25 one and has been extensively tested for Pose2Sim. \
You can also use the [BODY_135 model](https://github.com/CMU-Perceptual-Computing-Lab/openpose_train/tree/master/experimental_models), which allows for the evaluation of pronation/supination, wrist flexion, and wrist deviation.\
All other OpenPose models (BODY_25, COCO, MPII) are also supported.\
Make sure you modify the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file accordingly.
* Use one of the `json_display_with_img.py` or `json_display_with_img.py` scripts (see [Utilities](#utilities)) if you want to display 2D pose detections.
**N.B.:** *OpenPose BODY_25B is the default 2D pose estimation model used in Pose2Sim. However, other skeleton models from other 2D pose estimation solutions can be used alternatively.* \
- You will first need to convert your 2D detection files to the OpenPose format (see [Utilities](#utilities)). \
- Then, change the `pose_model` in the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. You may also need to choose a different `tracked_keypoint` if the Neck is not detected by the chosen model. \
[Mediapipe BlazePose](https://google.github.io/mediapipe/solutions/pose.html) is very fast, fully runs under Python, handles upside-down postures and wrist movements (but no subtalar ankle angles). \
However, it is less robust and accurate than OpenPose, and can only detect a single person.
* Use the script `Blazepose_runsave.py` (see [Utilities](#utilities)) to run BlazePose under Python, and store the detected coordinates in OpenPose (json) or DeepLabCut (h5 or csv) format:
* Make sure you change the `pose_model` and the `tracked_keypoint` in the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file.
If you need to detect specific points on a human being, an animal, or an object, you can also train your own model with [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut).
1. Train your DeepLabCut model and run it on your images or videos (more instruction on their repository)
2. Translate the h5 2D coordinates to json files (with `DLC_to_OpenPose.py` script, see [Utilities](#utilities)):
3. Report the model keypoints in the [skeleton.py](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/skeletons.py) file, and make sure you change the `pose_model` and the `tracked_keypoint` in the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file.
4. Create an OpenSim model if you need 3D joint angles.
### With AlphaPose:
[AlphaPose](https://github.com/MVIG-SJTU/AlphaPose) is one of the main competitors of OpenPose, and its accuracy is comparable. As a top-down approach (unlike OpenPose which is bottom-up), it is faster on single-person detection, but slower on multi-person detection.
* Install and run AlphaPose on your videos (more instruction on their repository)
* Translate the AlphaPose single json file to OpenPose frame-by-frame files (with `AlphaPose_to_OpenPose.py` script, see [Utilities](#utilities)):
* Make sure you change the `pose_model` and the `tracked_keypoint` in the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file.
If you already have a calibration file, set `calibration_type` type to `convert` in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file.
- set `convert_from` to 'qualisys' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. Change `binning_factor` to 2 if you film in 540p
- Use their C++ API [to retrieve extrinsic properties](https://docs.optitrack.com/developer-tools/motive-api/motive-api-function-reference#tt_cameraxlocation). Translation can be copied as is in your `Calib.toml` file, but TT_CameraOrientationMatrix first needs to be [converted to a Rodrigues vector](https://docs.opencv.org/3.4/d9/d0c/group__calib3d.html#ga61585db663d9da06b68e70cfbf6a1eac) with OpenCV. See instructions [here](https://github.com/perfanalytics/pose2sim/issues/28)
- set `convert_from` to 'vicon' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed.
> *N.B.:* Try the calibration tool on the Demo by changing `calibration_type` to `calculate` in [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml).\
For the sake of practicality, there are voluntarily few board images for intrinsic calibration, and few points to click for extrinsic calibration. In spite of this, your reprojection error should be under 1-2 cm, which [does not hinder the quality of kinematic results in practice](https://www.mdpi.com/1424-8220/21/19/6530/htm#:~:text=Angle%20results%20were,Table%203).).
> *N.B.:* _Intrinsic parameters:_ camera properties (focal length, optical center, distortion), usually need to be calculated only once in their lifetime. In theory, cameras with same model and same settings will have identical intrinsic parameters.\
> *N.B.:* If you already calculated intrinsic parameters earlier, you can skip this step. Copy your intrinsic parameters (`size`, `mat`, and `dist`) in a new `Calib*.toml` file, and set `overwrite_intrinsics` to false. Run Demo to obtain an example `Calib.toml` file.
> *N.B.:* _Extrinsic parameters:_ camera placement in space (position and orientation), need to be calculated every time a camera is moved. Can be calculated from a board, or from points in the scene with known coordinates.
It should preferably be larger than the one used for intrinsics, as results will not be very accurate out of the covered zone.
- **If you film the raw scene** (more flexible and potentially more accurate if points are spread out):\
Manually measure the 3D coordinates of 10 or more points in the scene (tiles, lines on wall, boxes, treadmill dimensions, etc). These points should be as spread out as possible.\
Then you will click on the corresponding image points for each view.
- For a more automatic calibration, OpenPose keypoints could also be used for calibration.\
[Want to contribute?](#how-to-contribute)
Open an Anaconda prompt or a terminal, type `ipython`.\
By default, `calibration()` 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.calibration(r'path_to_config.toml')`.
```
from Pose2Sim import Pose2Sim
Pose2Sim.calibration()
```
Output:\
<imgsrc="Content/Calib2D.png"width="760">
<imgsrc="Content/CalibFile.png"width="760">
<details>
<summary>The project hierarchy becomes: (CLICK TO SHOW)</summary>
If your cameras are not natively synchronized, you can use [this script](https://github.com/perfanalytics/pose2sim/blob/draft/Pose2Sim/Utilities/synchronize_cams.py).\
Alternatively, use a clap, a flash, or a beep noise to synchronize them.
> _**Track the person viewed by the most cameras, in case of several detections by OpenPose.**_ \
*N.B.: Skip this step if only one person is in the field of view.*\
> [Want to contribute?](#how-to-contribute) _**Allow for multiple person analysis.**_
Open an Anaconda prompt or a terminal, type `ipython`.\
By default, `personAssociation()` 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.personAssociation(r'path_to_config.toml')`.
Check printed output. If results are not satisfying, try and release the constraints in the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file.
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')`.
```
from Pose2Sim import Pose2Sim
Pose2Sim.triangulation()
```
Check printed output, and vizualise your trc in OpenSim: `File -> Preview experimental data`.\
If your triangulation is not satisfying, try and release the constraints in the `Config.toml` file.
Output:\
<imgsrc="Content/Triangulate3D.png"width="760">
<details>
<summary>The project hierarchy becomes: (CLICK TO SHOW)</summary>
> _**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`.\
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')`.
```
from Pose2Sim import Pose2Sim
Pose2Sim.filtering()
```
Check your filtration with the displayed figures, and vizualise your trc in OpenSim. If your filtering is not satisfying, try and change the parameters in the `Config.toml` file.
Output:\
<imgsrc="Content/FilterPlot.png"width="760">
<imgsrc="Content/Filter3D.png"width="760">
<details>
<summary>The project hierarchy becomes: (CLICK TO SHOW)</summary>
3. Load the provided `IK_Setup_Pose2Sim_Body25b.xml` scaling file from `pose2sim/Empty_project/opensim`. *(Tools -> Inverse kinematics -> Load)*
4. Replace the example .trc file with your own data, and specify the path to your angle kinematics output file.
5. Run
6. Motion results will appear as .mot file in the `pose2sim/Empty_project/opensim` directory (automatically saved).
<imgsrc="Content/OpenSim.JPG"width="380">
### Command line
Alternatively, you can use command-line tools:
- Open an Anaconda terminal in your OpenSim/bin directory, typically `C:\OpenSim <Version>\bin`.\
You'll need to adjust the `time_range`, `output_motion_file`, and enter the full paths to the input and output `.osim`, `.trc`, and `.mot` files in your setup file.
- Or take advantage of the full the OpenSim Python API. See [there](https://simtk-confluence.stanford.edu:8443/display/OpenSim/Scripting+in+Python) for installation instructions (conda install may take a while).\
Make sure to replace `38` in `py38np120` with your Python version (3.8 in this case).
If you run into a DLL error while importing opensim, open the file `<Pose2Sim-env>\Lib\opensim\__init__.py` and replace `conda`by `conda-meta` line 4. `<Pose2Sim-env>` location can be found with `conda env list`.\
You can also run other API commands. See [there](https://simtk-confluence.stanford.edu:8443/display/OpenSim/Common+Scripting+Commands#CommonScriptingCommands-UsingtheTools) for more instructions on how to use it.
If you need to batch process multiple data or with multiple different parameters, you can run any Pose2Sim function with a `config` dictionary instead of a file. For example:
A list of standalone tools (see [Utilities](https://github.com/perfanalytics/pose2sim/tree/main/Pose2Sim/Utilities)), which can be either run as scripts, or imported as functions. Check usage in the docstrings of each Python file. The figure below shows how some of these toolscan be used to further extend Pose2Sim usage.
<details>
<summary><b>Converting files and Calibrating</b> (CLICK TO SHOW)</summary>
Converts 3D point data of a .c3d file to a .trc file compatible with OpenSim. No analog data (force plates, emg) nor computed data (angles, powers, etc) are retrieved.
Converts a Qualisys .qca.txt calibration file to the Pose2Sim .toml calibration file (similar to what is used in [AniPose](https://anipose.readthedocs.io/en/latest/)).
Detects gait events from point coordinates according to [Zeni et al. (2008)](https://www.sciencedirect.com/science/article/abs/pii/S0966636207001804?via%3Dihub).
If you use this code or data, please cite [Pagnon et al., 2022b](https://doi.org/10.21105/joss.04362), [Pagnon et al., 2022a](https://www.mdpi.com/1424-8220/22/7/2712), or [Pagnon et al., 2021](https://www.mdpi.com/1424-8220/21/19/6530).
@Article{Pagnon_2022_JOSS,
AUTHOR = {Pagnon, David and Domalain, Mathieu and Reveret, Lionel},
TITLE = {Pose2Sim: An open-source Python package for multiview markerless kinematics},
If you want to contribute to Pose2Sim, please follow [this guide](https://docs.github.com/en/get-started/quickstart/contributing-to-projects) on how to fork, modify and push code, and submit a pull request. I would appreciate it if you provided as much useful information as possible about how you modified the code, and a rationale for why you're making this pull request. Please also specify on which operating system and on which Python version you have tested the code.
> - [x] **Pose:** Support OpenPose [body_25b](https://github.com/CMU-Perceptual-Computing-Lab/openpose_train/tree/master/experimental_models#body_25b-model---option-2-recommended) for more accuracy, [body_135](https://github.com/CMU-Perceptual-Computing-Lab/openpose_train/tree/master/experimental_models#single-network-whole-body-pose-estimation-model) for pronation/supination.
> - [x] **Pose:** Support [BlazePose](https://developers.google.com/mediapipe/solutions/vision/pose_landmarker) for faster inference (on mobile device).
> - [x] **Pose:** Support [DeepLabCut](http://www.mackenziemathislab.org/deeplabcut) for training on custom datasets.
> - [x] **Pose:** Support [AlphaPose](https://github.com/MVIG-SJTU/AlphaPose) as an alternative to OpenPose.
> - [ ] **Pose:** Support [MMPose](https://github.com/open-mmlab/mmpose), [SLEAP](https://sleap.ai/), etc.
> - [x] **Calibration:** Easier and clearer calibration procedure: separate intrinsic and extrinsic parameter calculation, edit corner detection if some are wrongly detected (or not visible).
> - [x] **Calibration:** Possibility to evaluate extrinsic parameters from cues on scene.
> - [ ] **Calibration:** Once object points have been detected or clicked once, track them for live calibration of moving cameras. Propose to click again when they are lost.
> - [ ] **Calibration:** Calculate calibration with points rather than board. (1) SBA calibration with wand (cf [Argus](https://argus.web.unc.edu), see converter [here](https://github.com/backyardbiomech/DLCconverterDLT/blob/master/DLTcameraPosition.py)). Set world reference frame in the end.
> - [ ] **Calibration:** Alternatively, self-calibrate with [OpenPose keypoints](https://ietresearch.onlinelibrary.wiley.com/doi/full/10.1049/cvi2.12130). Set world reference frame in the end.
> - [ ] **Person Association:** Multiple persons association. 1. Triangulate all the persons whose reprojection error is below a certain threshold (instead of only the one with minimum error), and then track in time with speed cf [Slembrouck 2020](https://link.springer.com/chapter/10.1007/978-3-030-40605-9_15)? or 2. Based on affinity matrices [Dong 2021](https://arxiv.org/pdf/1901.04111.pdf)? or 3. Based on occupancy maps [Yildiz 2012](https://link.springer.com/chapter/10.1007/978-3-642-35749-7_10)? or 4. With a neural network [Huang 2023](https://arxiv.org/pdf/2304.09471.pdf)?
> - [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 keypoint.
> - [x] **Triangulation:** Show how many cameras on average had to be excluded for each keypoint.
> - [ ] **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.
> - [ ] **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:** Solve limb swapping (although not really an issue with Body_25b) by using RANSAC or SDS triangulation ignoring right and left, and then decide which side points are by majority voting + giving more confidence to cameras whose plane is the most coplanar to the right/left line.
> - [ ] **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).
> - [x] **OpenSim:** Integrate better spine from [lifting fullbody model](https://pubmed.ncbi.nlm.nih.gov/30714401) to the [gait full-body model](https://nmbl.stanford.edu/wp-content/uploads/07505900.pdf), more accurate for the knee.
> - [x] **OpenSim:** Optimize model marker positions as compared to ground-truth marker-based positions.
> - [ ] **GUI:** Blender add-on (cf [MPP2SOS](https://blendermarket.com/products/mocap-mpp2soss)), or webapp (e.g., with [Napari](https://napari.org/stable). See my draft project [Maya-Mocap](https://github.com/davidpagnon/Maya-Mocap) and [BlendOsim](https://github.com/JonathanCamargo/BlendOsim).
> - [ ] **Bug:** common.py, class plotWindow(). Python crashes after a few runs of `Pose2Sim.filtering()` when `display_figures=true`. See [there](https://github.com/superjax/plotWindow/issues/7).
> - [ ] **Bug:** calibration.py. FFMPEG error message when calibration files are images. See [there](https://github.com/perfanalytics/pose2sim/issues/33#:~:text=In%20order%20to%20check,filter%20this%20message%20yet.).
</br>
**Pose2Sim releases:**
> - v0.1: Published online
> - v0.2: Published associated paper
> - v0.3: Supported other pose estimation algorithms
