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support opencap and biocv calibration

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This commit is contained in:
davidpagnon 2023-09-21 14:33:17 +02:00
parent f3cff42d5c
commit afed272759
3 changed files with 109 additions and 15 deletions
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2
Pose2Sim/Demo/User/Config.toml
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@ -35,7 +35,7 @@ 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', 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

120
Pose2Sim/calibration.py
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@ -24,7 +24,6 @@
OUTPUTS:
- a calibration file in the 'calibration' folder (.toml extension)
'''
# TODO: DETECT WHEN WINDOW IS CLOSED
@ -37,6 +36,7 @@ from Pose2Sim.common import RT_qca2cv, rotate_cam, quat2mat, euclidean_distance,
import os
import logging
import pickle
import numpy as np
os.environ["OPENCV_LOG_LEVEL"]="FATAL"
import cv2
@ -95,7 +95,6 @@ def calib_qca_fun(file_to_convert_path, binning_factor=1):
- 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
'''
logging.info(f'Converting {file_to_convert_path} to .toml calibration file...')
@ -111,7 +110,7 @@ def calib_qca_fun(file_to_convert_path, binning_factor=1):
R = [np.array(cv2.Rodrigues(r)[0]).flatten() for r in R]
T = np.array(T)
return ret, C, S, D, K, R, T
@ -216,7 +215,6 @@ def calib_optitrack_fun(config):
- 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
'''
pass
@ -240,7 +238,6 @@ def calib_vicon_fun(file_to_convert_path, binning_factor=1):
- 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
'''
logging.info(f'Converting {file_to_convert_path} to .toml calibration file...')
@ -324,6 +321,92 @@ def read_vicon(vicon_path):
return ret, C, S, D, K, R, T
def calib_biocv_fun(file_to_convert_paths, binning_factor=1):
'''
Convert bioCV calibration files.
INPUTS:
- file_to_convert_path: path of the calibration files to convert (no extension)
- binning_factor: always 1 with biocv 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
'''
logging.info(f'Converting {[os.path.basename(f) for f in file_to_convert_paths]} to .toml calibration file...')
ret, C, S, D, K, R, T = [], [], [], [], [], [], []
for i, f_path in enumerate(file_to_convert_paths):
with open(f_path) as f:
calib_data = f.read().split('\n')
ret += [np.nan]
C += [f'cam_{str(i+1).zfill(2)}']
S += [[int(calib_data[0]), int(calib_data[1])]]
D += [[float(d) for d in calib_data[-2].split(' ')[:4]]]
K += [np.array([k.strip().split(' ') for k in calib_data[2:5]], np.float32)]
RT = np.array([k.strip().split(' ') for k in calib_data[6:9]], np.float32)
R += [cv2.Rodrigues(RT[:,:3])[0].squeeze()]
T += [RT[:,3]/1000]
return ret, C, S, D, K, R, T
def calib_opencap_fun(file_to_convert_paths, binning_factor=1):
'''
Convert OpenCap calibration files.
Extrinsics in OpenCap are calculated with a vertical board for the world frame.
As we want the world frame to be horizontal, we need to rotate cameras by -Pi/2 around x in the world frame.
T is good the way it is.
INPUTS:
- file_to_convert_path: path of the .pickle calibration files to convert
- binning_factor: always 1 with biocv 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
'''
logging.info(f'Converting {[os.path.basename(f) for f in file_to_convert_paths]} to .toml calibration file...')
ret, C, S, D, K, R, T = [], [], [], [], [], [], []
for i, f_path in enumerate(file_to_convert_paths):
with open(f_path, 'rb') as f_pickle:
calib_data = pickle.load(f_pickle)
ret += [np.nan]
C += [f'cam_{str(i+1).zfill(2)}']
S += [list(calib_data['imageSize'].squeeze()[::-1])]
D += [list(calib_data['distortion'][0][:-1])]
K += [calib_data['intrinsicMat']]
R_cam = calib_data['rotation']
T_cam = calib_data['translation'].squeeze()
# Rotate cameras by Pi/2 around x in world frame
# camera frame to world frame
R_w, T_w = RT_qca2cv(R_cam, T_cam)
# x_rotate -Pi/2 and z_rotate Pi
R_w_90, T_w_90 = rotate_cam(R_w, T_w, ang_x=-np.pi/2, ang_y=0, ang_z=np.pi)
# world frame to camera frame
R_c_90, T_c_90 = RT_qca2cv(R_w_90, T_w_90)
# store in R and T
R+=[cv2.Rodrigues(R_c_90)[0].squeeze()]
T+=[T_cam/1000]
return ret, C, S, D, K, R, T
def calib_board_fun(calib_dir, intrinsics_config_dict, extrinsics_config_dict):
'''
Calibrates intrinsic and extrinsic parameters
@ -762,7 +845,7 @@ def imgp_objp_visualizer_clicker(img, imgp=[], objp=[], img_path=''):
elif count == len(objp)-1:
# if all objp have been clicked or indicated as not visible, close all
objp_confirmed = np.array([[objp[count]] if 'objp_confirmed' not in globals() else objp_confirmed+[objp[count]]][0])[:-1]
imgp_confirmed = np.expand_dims(scat.get_offsets(), axis=1)
imgp_confirmed = np.array(np.expand_dims(scat.get_offsets(), axis=1), np.float32)
plt.close('all')
for var_to_delete in ['events', 'count', 'scat', 'fig_3d', 'ax_3d', 'objp_confirmed_notok']:
if var_to_delete in globals():
@ -830,8 +913,8 @@ def imgp_objp_visualizer_clicker(img, imgp=[], objp=[], img_path=''):
# If last event was left click, remove last point and if objp given, from objp_confirmed
# If last event was 'H' and objp given, remove last point from objp_confirmed_notok
elif event.button == 3: # right click
# If last event was left click:
if 'events' in globals():
# If last event was left click:
if 'button' in dir(events[-1]):
if events[-1].button == 1:
# Remove lastpoint from image
@ -841,7 +924,8 @@ def imgp_objp_visualizer_clicker(img, imgp=[], objp=[], img_path=''):
# Remove last point from imgp_confirmed
imgp_confirmed = imgp_confirmed[:-1]
if len(objp) != 0:
if count >= 1: count -= 1
if count >= 0:
count -= 1
# Remove last point from objp_confirmed
objp_confirmed = objp_confirmed[:-1]
# remove from plot
@ -1030,13 +1114,13 @@ def recap_calibrate(ret, calib_path, calib_full_type):
if cam != 'metadata':
f_px = calib[cam]['matrix'][0][0]
Dm = euclidean_distance(calib[cam]['translation'], [0,0,0])
if calib_full_type=='convert_qualisys' or calib_full_type=='convert_vicon':
if calib_full_type in ['convert_qualisys', 'convert_vicon','convert_opencap', 'convert_biocv']:
ret_m.append( np.around(ret[c], decimals=3) )
ret_px.append( np.around(ret[c] / (Dm*1000) * f_px, decimals=3) )
elif calib_full_type=='calculate_board':
ret_px.append( np.around(ret[c], decimals=3) )
ret_m.append( np.around(ret[c]*Dm*1000 / f_px, decimals=3) )
logging.info(f'\n--> Residual (RMS) calibration errors for each camera are respectively {ret_px} px, \nwhich corresponds to {ret_m} mm.\n')
logging.info(f'Calibration file is stored at {calib_path}.')
@ -1066,16 +1150,24 @@ def calibrate_cams_all(config):
convert_filetype = config.get('calibration').get('convert').get('convert_from')
if convert_filetype=='qualisys':
convert_ext = '.qca.txt'
file_to_convert_path = glob.glob(os.path.join(calib_dir, f'*{convert_ext}*'))[0]
binning_factor = config.get('calibration').get('convert').get('qualisys').get('binning_factor')
elif convert_filetype=='optitrack':
logging.info('See Readme.md to retrieve Optitrack calibration values.')
elif convert_filetype=='vicon':
convert_ext = '.xcp'
file_to_convert_path = glob.glob(os.path.join(calib_dir, f'*{convert_ext}*'))[0]
binning_factor = 1
file_to_convert_path = glob.glob(os.path.join(calib_dir, f'*{convert_ext}*'))[0]
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=='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]=='']
file_to_convert_path = [os.path.join(calib_dir,f) for f in list_dir_noext if os.path.isfile(os.path.join(calib_dir, f))]
binning_factor = 1
calib_output_path = os.path.join(calib_dir, f'Calib_{convert_filetype}.toml')
calib_full_type = '_'.join([calib_type, convert_filetype])
args_calib_fun = [file_to_convert_path, binning_factor]
@ -1105,6 +1197,8 @@ def calibrate_cams_all(config):
'convert_qualisys': calib_qca_fun,
'convert_optitrack': calib_optitrack_fun,
'convert_vicon': calib_vicon_fun,
'convert_opencap': calib_opencap_fun,
'convert_biocv': calib_biocv_fun,
'calculate_board': calib_board_fun,
'calculate_points': calib_points_fun
}

2
README.md
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@ -809,7 +809,7 @@ If you want to contribute to Pose2Sim, please follow [this guide](https://docs.g
- Supervised my PhD: @lreveret (INRIA, Université Grenoble Alpes), and @mdomalai (Université de Poitiers).
- Provided the Demo data: @aaiaueil from Université Gustave Eiffel.
- Tested the code and provided feedback: @simonozan
- Tested the code and provided feedback: @simonozan, @daeyongyang, @ANaaim, @rlagnsals
- Provided a code snippet for Optitrack calibration: @claraaudap (Université Bretagne Sud).
- Issued MPP2SOS, a (non-free) Blender extension based on Pose2Sim: @carlosedubarreto