convert easymocap calibration files

Pose2Sim/Demo/User/Config.toml

@@ -35,12 +35,13 @@ openpose_path = '' # only checked if OpenPose is used
 calibration_type = 'convert' # 'convert' or 'calculate'
 
    [calibration.convert]
-   convert_from = 'qualisys' # 'qualisys', 'optitrack', vicon', 'opencap', or 'biocv'
+   convert_from = 'qualisys' # 'qualisys', 'optitrack', vicon', 'opencap', 'easymocap', or 'biocv'
       [calibration.convert.qualisys]
       binning_factor = 1 # Usually 1, except when filming in 540p where it usually is 2
       [calibration.convert.optitrack]  # See readme for instructions
       [calibration.convert.vicon]      # No parameters needed
       [calibration.convert.opencap]    # No parameters needed
+      [calibration.convert.easymocap]    # No parameters needed
       [calibration.convert.biocv]      # No parameters needed
   
 

Pose2Sim/Demo/User/test.toml

@@ -35,9 +35,14 @@ openpose_path = '' # only checked if OpenPose is used
 calibration_type = 'convert' # 'convert' or 'calculate'
 
    [calibration.convert]
-   convert_from = 'qualisys' # 'qualisys', 'optitrack', or 'vicon'
+   convert_from = 'qualisys' # 'qualisys', 'optitrack', vicon', 'opencap', 'easymocap', or 'biocv'
       [calibration.convert.qualisys]
       binning_factor = 1 # Usually 1, except when filming in 540p where it usually is 2
+      [calibration.convert.optitrack]  # See readme for instructions
+      [calibration.convert.vicon]      # No parameters needed
+      [calibration.convert.opencap]    # No parameters needed
+      [calibration.convert.easymocap]    # No parameters needed
+      [calibration.convert.biocv]      # No parameters needed
   
 
    [calibration.calculate] 

Pose2Sim/Empty_project/User/Config.toml

@@ -35,9 +35,14 @@ openpose_path = '' # only checked if OpenPose is used
 calibration_type = 'convert' # 'convert' or 'calculate'
 
    [calibration.convert]
-   convert_from = 'qualisys' # 'qualisys', 'optitrack', or 'vicon'
+   convert_from = 'qualisys' # 'qualisys', 'optitrack', vicon', 'opencap', 'easymocap', or 'biocv'
       [calibration.convert.qualisys]
       binning_factor = 1 # Usually 1, except when filming in 540p where it usually is 2
+      [calibration.convert.optitrack]  # See readme for instructions
+      [calibration.convert.vicon]      # No parameters needed
+      [calibration.convert.opencap]    # No parameters needed
+      [calibration.convert.easymocap]    # No parameters needed
+      [calibration.convert.biocv]      # No parameters needed
   
 
    [calibration.calculate] 

Pose2Sim/Utilities/calib_easymocap_to_toml.py

@@ -4,7 +4,7 @@
 
 '''
     ##################################################
-    ## YML CALIBRATION TO TOML CALIBRATION          ##
+    ## EASYMOCAP CALIBRATION TO TOML CALIBRATION    ##
     ##################################################
     
     Converts OpenCV intrinsic and extrinsic .yml calibration files 
@@ -14,9 +14,9 @@
     Please correct in the resulting .toml file if needed. Take your image size as a reference.
     
     Usage: 
-        import calib_yml_to_toml; calib_yml_to_toml.calib_yml_to_toml_func(r'<intrinsic_yml_file>', r'<extrinsic_yml_file>')
+        import calib_easymocap_to_toml; calib_yml_to_toml.calib_easymocap_to_toml_func(r'<intrinsic_yml_file>', r'<extrinsic_yml_file>')
-        OR python -m calib_yml_to_toml -i intrinsic_yml_file -e extrinsic_yml_file
+        OR python -m calib_easymocap_to_toml -i intrinsic_yml_file -e extrinsic_yml_file
-        OR python -m calib_yml_to_toml -i intrinsic_yml_file -e extrinsic_yml_file -o output_toml_file
+        OR python -m calib_easymocap_to_toml -i intrinsic_yml_file -e extrinsic_yml_file -o output_toml_file
 '''
 
 
@@ -113,7 +113,7 @@ def toml_write(toml_path, C, S, D, K, R, T):
         cal_f.write(meta)
 
 
-def calib_yml_to_toml_func(*args):
+def calib_easymocap_to_toml_func(*args):
     '''
     Converts OpenCV intrinsic and extrinsic .yml calibration files 
     to an OpenCV .toml calibration file
@@ -146,10 +146,10 @@ def calib_yml_to_toml_func(*args):
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
-    parser.add_argument('-i', '--intrinsic_file', required = True, help='OpenCV intrinsic .yml calibration file')
+    parser.add_argument('-i', '--intrinsic_file', required = True, help='EasyMocap intrinsic .yml calibration file')
-    parser.add_argument('-e', '--extrinsic_file', required = True, help='OpenCV extrinsic .yml calibration file')
+    parser.add_argument('-e', '--extrinsic_file', required = True, help='EasyMocap extrinsic .yml calibration file')
     parser.add_argument('-t', '--toml_file', required=False, help='OpenCV .toml output calibration file')
     args = vars(parser.parse_args())
     
-    calib_yml_to_toml_func(args)
+    calib_easymocap_to_toml_func(args)
     

Pose2Sim/Utilities/calib_toml_to_easymocap.py

@@ -4,16 +4,16 @@
 
 '''
     ##################################################
-    ## YML CALIBRATION TO TOML CALIBRATION          ##
+    ## EASYMOCAP CALIBRATION TO TOML CALIBRATION    ##
     ##################################################
     
-    Convert an OpenCV .toml calibration file 
+    Convert a Pose2Sim .toml calibration file 
-    to OpenCV intrinsic and extrinsic .yml calibration files 
+    to EasyMocap intrinsic and extrinsic .yml calibration files 
 
     Usage: 
-        from Pose2Sim.Utilities import calib_toml_to_yml; calib_toml_to_yml.calib_toml_to_yml_func(r'<input_toml_file>')
+        from Pose2Sim.Utilities import calib_toml_to_easymocap; calib_toml_to_easymocap.calib_toml_to_easymocap_func(r'<input_toml_file>')
-        OR python -m calib_yml_to_toml -t input_toml_file
+        OR python -m calib_easymocap_to_toml -t input_toml_file
-        OR python -m calib_yml_to_toml -t input_toml_file -i intrinsic_yml_file -e extrinsic_yml_file
+        OR python -m calib_easymocap_to_toml -t input_toml_file -i intrinsic_yml_file -e extrinsic_yml_file
 '''
 
 ## INIT
@@ -61,6 +61,7 @@ def read_toml(toml_path):
 
     return C, S, D, K, R, T
 
+
 def write_intrinsic_yml(intrinsic_yml_path, C, D, K):
     '''
     Writes an OpenCV .yml intrinsic calibration file
@@ -109,15 +110,16 @@ def write_extrinsic_yml(extrinsic_yml_path, C, R, T):
         
     extrinsic_file.release()
 
-def calib_toml_to_yml_func(*args):
+
+def calib_toml_to_easymocap_func(*args):
     '''
-    Convert an OpenCV .toml calibration file 
+    Convert a Pose2Sim .toml calibration file 
-    to OpenCV intrinsic and extrinsic .yml calibration files 
+    to EasyMocap intrinsic and extrinsic .yml calibration files 
 
     Usage: 
-        import calib_toml_to_yml; calib_toml_to_yml.calib_toml_to_yml_func(r'<input_toml_file>')
+        from Pose2Sim.Utilities import calib_toml_to_easymocap; calib_toml_to_easymocap.calib_toml_to_easymocap_func(r'<input_toml_file>')
-        OR python -m calib_toml_to_yml -t input_toml_file
+        OR python -m calib_easymocap_to_toml -t input_toml_file
-        OR python -m calib_toml_to_yml -t input_toml_file -i intrinsic_yml_file -e extrinsic_yml_file
+        OR python -m calib_easymocap_to_toml -t input_toml_file -i intrinsic_yml_file -e extrinsic_yml_file
     '''
     
     try:
@@ -147,5 +149,5 @@ if __name__ == '__main__':
     parser.add_argument('-e', '--extrinsic_yml_file', required = False, help='OpenCV extrinsic .yml calibration file')
     args = vars(parser.parse_args())
     
-    calib_toml_to_yml_func(args)
+    calib_toml_to_easymocap_func(args)
 

Pose2Sim/calibration.py

@@ -321,12 +321,77 @@ def read_vicon(vicon_path):
     return ret, C, S, D, K, R, T
 
 
-def calib_biocv_fun(file_to_convert_paths, binning_factor=1):
+def read_intrinsic_yml(intrinsic_path):
+    '''
+    Reads an intrinsic .yml calibration file
+    Returns 3 lists of size N (N=number of cameras):
+    - S (image size)
+    - K (intrinsic parameters)
+    - D (distorsion)
+
+    N.B. : Size is calculated as twice the position of the optical center. Please correct in the .toml file if needed.
+    '''
+    intrinsic_yml = cv2.FileStorage(intrinsic_path, cv2.FILE_STORAGE_READ)
+    N = intrinsic_yml.getNode('names').size()
+    S, D, K = [], [], []
+    for i in range(N):
+        name = intrinsic_yml.getNode('names').at(i).string()
+        K.append(intrinsic_yml.getNode(f'K_{name}').mat())
+        D.append(intrinsic_yml.getNode(f'dist_{name}').mat().flatten()[:-1])
+        S.append([K[i][0,2]*2, K[i][1,2]*2])
+    return S, K, D
+    
+
+def read_extrinsic_yml(extrinsic_path):
+    '''
+    Reads an intrinsic .yml calibration file
+    Returns 3 lists of size N (N=number of cameras):
+    - R (extrinsic rotation, Rodrigues vector)
+    - T (extrinsic translation)
+    '''
+    extrinsic_yml = cv2.FileStorage(extrinsic_path, cv2.FILE_STORAGE_READ)
+    N = extrinsic_yml.getNode('names').size()
+    R, T = [], []
+    for i in range(N):
+        name = extrinsic_yml.getNode('names').at(i).string()
+        R.append(extrinsic_yml.getNode(f'R_{name}').mat().flatten()) # R_1 pour Rodrigues, Rot_1 pour matrice
+        T.append(extrinsic_yml.getNode(f'T_{name}').mat().flatten())
+    return R, T
+
+
+def calib_easymocap_fun(files_to_convert_paths, binning_factor=1):
+    '''
+    Reads EasyMocap .yml calibration files
+
+    INPUTS:
+    - files_to_convert_paths: paths of the intri.yml and extri.yml calibration files to convert
+    - binning_factor: always 1 with easymocap calibration
+
+    OUTPUTS:
+    - ret: residual reprojection error in _mm_: list of floats
+    - C: camera name: list of strings
+    - S: image size: list of list of floats
+    - D: distorsion: list of arrays of floats
+    - K: intrinsic parameters: list of 3x3 arrays of floats
+    - R: extrinsic rotation: list of arrays of floats
+    - T: extrinsic translation: list of arrays of floats
+    '''
+
+    extrinsic_path, intrinsic_path = files_to_convert_paths
+    S, K, D = read_intrinsic_yml(intrinsic_path)
+    R, T = read_extrinsic_yml(extrinsic_path)
+    C = np.array(range(len(S)))+1
+    ret = [np.nan]*len(C)
+    
+    return ret, C, S, D, K, R, T
+
+
+def calib_biocv_fun(files_to_convert_paths, binning_factor=1):
     '''
     Convert bioCV calibration files.
 
     INPUTS:
-    - file_to_convert_path: path of the calibration files to convert (no extension)
+    - files_to_convert_paths: paths of the calibration files to convert (no extension)
     - binning_factor: always 1 with biocv calibration
 
     OUTPUTS:
@@ -339,10 +404,10 @@ def calib_biocv_fun(file_to_convert_paths, binning_factor=1):
     - T: extrinsic translation: list of arrays of floats
     '''
     
-    logging.info(f'Converting {[os.path.basename(f) for f in file_to_convert_paths]} to .toml calibration file...')
+    logging.info(f'Converting {[os.path.basename(f) for f in files_to_convert_paths]} to .toml calibration file...')
 
     ret, C, S, D, K, R, T = [], [], [], [], [], [], []
-    for i, f_path in enumerate(file_to_convert_paths):
+    for i, f_path in enumerate(files_to_convert_paths):
         with open(f_path) as f:
             calib_data = f.read().split('\n')
             ret += [np.nan]
@@ -357,7 +422,7 @@ def calib_biocv_fun(file_to_convert_paths, binning_factor=1):
     return ret, C, S, D, K, R, T
 
 
-def calib_opencap_fun(file_to_convert_paths, binning_factor=1):
+def calib_opencap_fun(files_to_convert_paths, binning_factor=1):
     '''
     Convert OpenCap calibration files.
     
@@ -366,8 +431,8 @@ def calib_opencap_fun(file_to_convert_paths, binning_factor=1):
     T is good the way it is.
 
     INPUTS:
-    - file_to_convert_path: path of the .pickle calibration files to convert
+    - files_to_convert_paths: paths of the .pickle calibration files to convert
-    - binning_factor: always 1 with biocv calibration
+    - binning_factor: always 1 with opencap calibration
 
     OUTPUTS:
     - ret: residual reprojection error in _mm_: list of floats
@@ -379,10 +444,10 @@ def calib_opencap_fun(file_to_convert_paths, binning_factor=1):
     - T: extrinsic translation: list of arrays of floats
     '''
     
-    logging.info(f'Converting {[os.path.basename(f) for f in file_to_convert_paths]} to .toml calibration file...')
+    logging.info(f'Converting {[os.path.basename(f) for f in files_to_convert_paths]} to .toml calibration file...')
     
     ret, C, S, D, K, R, T = [], [], [], [], [], [], []
-    for i, f_path in enumerate(file_to_convert_paths):
+    for i, f_path in enumerate(files_to_convert_paths):
         with open(f_path, 'rb') as f_pickle:
             calib_data = pickle.load(f_pickle)
             ret += [np.nan]
@@ -393,7 +458,7 @@ def calib_opencap_fun(file_to_convert_paths, binning_factor=1):
             R_cam = calib_data['rotation']
             T_cam = calib_data['translation'].squeeze()
             
-            # Rotate cameras by Pi/2 around x in world frame
+            # Rotate cameras by Pi/2 around x in world frame -> could have just switched some columns in matrix
             # camera frame to world frame
             R_w, T_w = RT_qca2cv(R_cam, T_cam)
             # x_rotate -Pi/2 and z_rotate Pi
@@ -1161,6 +1226,9 @@ def calibrate_cams_all(config):
         elif convert_filetype=='opencap': # all files with .pickle extension
             file_to_convert_path = glob.glob(os.path.join(calib_dir, '*.pickle'))
             binning_factor = 1
+        elif convert_filetype=='easymocap': #intri.yml and intri.yml
+            file_to_convert_path = glob.glob(os.path.join(calib_dir, '*.yml'))
+            binning_factor = 1
         elif convert_filetype=='biocv': # all files without extension
             list_dir = os.listdir(calib_dir)
             list_dir_noext = [os.path.splitext(f)[0] for f in list_dir if os.path.splitext(f)[1]=='']	
@@ -1198,6 +1266,7 @@ def calibrate_cams_all(config):
         'convert_optitrack': calib_optitrack_fun,
         'convert_vicon': calib_vicon_fun,
         'convert_opencap': calib_opencap_fun,
+        'convert_easymocap': calib_easymocap_fun,
         'convert_biocv': calib_biocv_fun,
         'calculate_board': calib_board_fun,
         'calculate_points': calib_points_fun

README.md

@@ -41,7 +41,7 @@ If you can only use one single camera and don't mind losing some accuracy, pleas
       3. [With DeepLabCut](#with-deeplabcut)
       4. [With AlphaPose](#with-alphapose)
    3. [Camera calibration](#camera-calibration)
-      1. [Convert from Qualisys, Optitrack, Vicon, OpenCap, or bioCV](#convert-from-qualisys-optitrack-vicon-opencap-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)
    4. [Camera synchronization](#camera-synchronization)
    5. [Tracking, Triangulating, Filtering](#tracking-triangulating-filtering)
@@ -241,23 +241,26 @@ N.B.: Markers are not needed in Pose2Sim and were used here for validation
 > _**Convert a preexisting calibration file, or calculate intrinsic and extrinsic parameters from scratch.**_ \
 > _**N.B.:**_ You can visualize camera calibration in 3D with my (experimental) [Maya-Mocap tool](https://github.com/davidpagnon/Maya-Mocap). 
 
-### Convert from Qualisys, Optitrack, Vicon, OpenCap, or bioCV
+### Convert from Qualisys, Optitrack, Vicon, OpenCap, EasyMocap, or bioCV
       
 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.
-- **From Qualisys:**
+- **From [Qualisys](https://www.qualisys.com):**
   - Export calibration to `.qca.txt` within QTM.
   - Copy it in the `calibration` Pose2Sim folder.
   - 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.
-- **From Optitrack:** Exporting calibration will be available in Motive 3.2. In the meantime:
+- **From [Optitrack](https://optitrack.com/):** Exporting calibration will be available in Motive 3.2. In the meantime:
   - Calculate intrinsics with a board (see next section).
   - 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).
-- **From Vicon:**  
+- **From [Vicon](http://www.vicon.com/Software/Nexus):**  
   - Copy your `.xcp` Vicon calibration file to the Pose2Sim `calibration` folder.
   - 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.
-- **From OpenCap:**  
+- **From [OpenCap](https://www.opencap.ai/):**  
   - Copy your `.pickle` OpenCap calibration files to the Pose2Sim `calibration` folder.
   - set `convert_from` to 'opencap' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed.
-- **From bioCV:**  
+- **From [EasyMocap](https://github.com/zju3dv/EasyMocap/):**  
+  - Copy your `intri.yml` and `extri.yml` files to the Pose2Sim `calibration` folder.
+  - set `convert_from` to 'easymocap' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed.
+- **From [bioCV](https://github.com/camera-mc-dev/.github/blob/main/profile/mocapPipe.md):**  
   - Copy your bioCV calibration files (no extension) to the Pose2Sim `calibration` folder.
   - set `convert_from` to 'biocv' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed.
 
@@ -728,11 +731,11 @@ Converts a Qualisys .qca.txt calibration file to the Pose2Sim .toml calibration
 [calib_toml_to_qca.py](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Utilities/calib_toml_to_qca.py)
 Converts a Pose2Sim .toml calibration file (e.g., from a checkerboard) to a Qualisys .qca.txt calibration file.
 
-[calib_yml_to_toml.py](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Utilities/calib_yml_to_toml.py)
+[calib_easymocap_to_toml.py](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Utilities/calib_easymocap_to_toml.py)
-Converts OpenCV intrinsic and extrinsic .yml calibration files to an OpenCV .toml calibration file.
+Converts EasyMocap intrinsic and extrinsic .yml calibration files to an OpenCV .toml calibration file.
 
-[calib_toml_to_yml.py](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Utilities/calib_toml_to_yml.py)
+[calib_easymocap_to_yml.py](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Utilities/calib_toml_to_easymocap.py)
-Converts an OpenCV .toml calibration file to OpenCV intrinsic and extrinsic .yml calibration files.
+Converts an OpenCV .toml calibration file to EasyMocap intrinsic and extrinsic .yml calibration files.
    </pre>
 </details>
 
@@ -840,13 +843,13 @@ If you want to contribute to Pose2Sim, please follow [this guide](https://docs.g
 > - [x] **Calibration:** Convert [Optitrack](https://optitrack.com/) extrinsic calibration file.
 > - [x] **Calibration:** Convert [Vicon](http://www.vicon.com/Software/Nexus) .xcp calibration file.
 > - [x] **Calibration:** Convert [OpenCap](https://www.opencap.ai/) .pickle calibration files.
+> - [x] **Calibration:** Convert [EasyMocap](https://github.com/zju3dv/EasyMocap/) .yml calibration files.
 > - [x] **Calibration:** Convert [bioCV](https://github.com/camera-mc-dev/.github/blob/main/profile/mocapPipe.md) calibration files.
 > - [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:** Fine-tune calibration with bundle adjustment.
 > - [ ] **Calibration:** Support ChArUco board detection (see [there](https://mecaruco2.readthedocs.io/en/latest/notebooks_rst/Aruco/sandbox/ludovic/aruco_calibration_rotation.html)).
-> - [ ] **Calibration:** Convert bioCV (University of Bath) and OpenCap calibrations.
 > - [ ] **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.