diff --git a/Pose2Sim/Demo/S00_Demo_Session/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/Config.toml index 054e2e6..c5b43ff 100644 --- a/Pose2Sim/Demo/S00_Demo_Session/Config.toml +++ b/Pose2Sim/Demo/S00_Demo_Session/Config.toml @@ -30,7 +30,7 @@ exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['< [calibration] -calibration_type = 'convert' # 'convert' or 'calculate' +calibration_type = 'calculate' # 'convert' or 'calculate' [calibration.convert] convert_from = 'qualisys' # 'qualisys', 'optitrack', vicon', 'opencap', 'easymocap', 'biocv', 'anipose', or 'freemocap' diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/Calib_qualisys.toml b/Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/Calib_qualisys.toml deleted file mode 100644 index f291f73..0000000 --- a/Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/Calib_qualisys.toml +++ /dev/null @@ -1,39 +0,0 @@ -[cam_01] -name = "cam_01" -size = [ 1088.0, 1920.0] -matrix = [ [ 1681.244873046875, 0.0, 532.97369384375], [ 0.0, 1681.075439453125, 948.137390140625], [ 0.0, 0.0, 1.0]] -distortions = [ -0.000721609375, 0.002187234375, 9.5e-06, 1.078125e-05] -rotation = [ 1.6882754799999993, 1.0483220499999997, -0.41955852000000016] -translation = [ 0.3211048899999996, 0.9563320600000009, 2.8907130499999996] -fisheye = false - -[cam_02] -name = "cam_02" -size = [ 1088.0, 1920.0] -matrix = [ [ 1673.729614265625, 0.0, 534.494567875], [ 0.0, 1673.79724121875, 963.225891109375], [ 0.0, 0.0, 1.0]] -distortions = [ -0.000747609375, 0.00213728125, 1.51875e-05, 4.546875e-06] -rotation = [ 1.34975875, 1.5963809099999993, -1.1983285799999999] -translation = [ -0.11152829000000017, 0.7766184800000001, 3.0675519599999994] -fisheye = false - -[cam_03] -name = "cam_03" -size = [ 1088.0, 1920.0] -matrix = [ [ 1681.598388671875, 0.0, 513.20837403125], [ 0.0, 1681.509887703125, 955.005126953125], [ 0.0, 0.0, 1.0]] -distortions = [ -0.000729765625, 0.00215034375, -8.46875e-06, -8.078125e-06] -rotation = [ 0.8109654899999995, -2.1972129299999996, 1.3760277799999996] -translation = [ -0.7934803899999996, 0.32283594000000126, 4.353514870000001] -fisheye = false - -[cam_04] -name = "cam_04" -size = [ 1088.0, 1920.0] -matrix = [ [ 1675.234985359375, 0.0, 540.106201171875], [ 0.0, 1675.204223640625, 964.0302734375], [ 0.0, 0.0, 1.0]] -distortions = [ -0.000744265625, 0.002104171875, 4.328125e-06, 3.109375e-06] -rotation = [ 1.4045571699999995, -1.3887412699999993, 0.42535743000000026] -translation = [ 0.5030217200000007, 0.04894934000000083, 4.406564460000002] -fisheye = false - -[metadata] -adjusted = false -error = 0.0 diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/extrinsics/ext_cam1_img/.gitkeep b/Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/extrinsics/ext_cam01_img/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/extrinsics/ext_cam1_img/.gitkeep rename to 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a/Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/intrinsics/int_cam4_img/cam04_06_int.jpg b/Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/intrinsics/int_cam04_img/cam04_06_int.jpg similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/intrinsics/int_cam4_img/cam04_06_int.jpg rename to Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/intrinsics/int_cam04_img/cam04_06_int.jpg diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/intrinsics/int_cam4_img/cam04_07_int.jpg b/Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/intrinsics/int_cam04_img/cam04_07_int.jpg similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/intrinsics/int_cam4_img/cam04_07_int.jpg rename to Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/intrinsics/int_cam04_img/cam04_07_int.jpg diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml index c31ef68..99d62ce 100644 --- a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml +++ b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml @@ -119,7 +119,7 @@ # tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py ## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) # reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 +# likelihood_error_threshold_association = 0.2 # [triangulation] diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml index 0997e7c..4aa3e36 100644 --- a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml +++ b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml @@ -119,7 +119,7 @@ # tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py ## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) # reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 +# likelihood_error_threshold_association = 0.2 # [triangulation] diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00000.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00000.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00000.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00000.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00001.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00001.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00001.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00001.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00002.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00002.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00002.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00002.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00003.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00003.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00003.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00003.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00004.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00004.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00004.json rename to 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a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00010.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00010.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00010.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00010.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00011.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam01_json/Static_cam_01.00011.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam1_json/Static_cam_01.00011.json rename to 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a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam2_json/Static_cam_02.00005.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam02_json/Static_cam_02.00005.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam2_json/Static_cam_02.00005.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam02_json/Static_cam_02.00005.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam2_json/Static_cam_02.00006.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam02_json/Static_cam_02.00006.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam2_json/Static_cam_02.00006.json rename to 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a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00000.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00000.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00000.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00000.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00001.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00001.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00001.json rename to 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b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00005.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00005.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00005.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00006.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00006.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00006.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00006.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00007.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00007.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00007.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00007.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00008.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00008.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00008.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00008.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00009.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00009.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00009.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00009.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00010.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00010.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00010.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00010.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00011.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00011.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam3_json/Static_cam_03.00011.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam03_json/Static_cam_03.00011.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00000.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00000.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00000.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00000.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00001.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00001.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00001.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00001.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00002.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00002.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00002.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00002.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00003.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00003.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00003.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00003.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00004.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00004.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00004.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00004.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00005.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00005.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00005.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00005.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00006.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00006.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00006.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00006.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00007.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00007.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00007.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00007.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00008.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00008.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00008.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00008.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00009.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00009.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00009.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00009.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00010.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00010.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00010.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00010.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00011.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00011.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam4_json/Static_cam_04.00011.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/pose/cam04_json/Static_cam_04.00011.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml index 2932041..4a4cc14 100644 --- a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml +++ b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml @@ -119,7 +119,7 @@ # tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py ## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) # reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 +# likelihood_error_threshold_association = 0.2 # [triangulation] diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0000.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0000.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0000.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0000.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0001.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0001.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0001.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0001.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0002.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0002.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0002.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0002.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0003.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0003.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0003.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0003.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0004.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0004.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0004.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0004.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0005.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0005.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0005.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0005.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0006.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0006.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0006.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0006.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0007.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0007.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0007.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0007.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0008.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0008.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0008.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam01_json/cam01.0008.json diff --git 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a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0087.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0087.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0087.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0087.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0088.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0088.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0088.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0088.json diff --git 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a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0091.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0091.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0091.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0091.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0092.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0092.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0092.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0092.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0093.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0093.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0093.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0093.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0094.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0094.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0094.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0094.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0095.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0095.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0095.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0095.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0096.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0096.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0096.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0096.json diff --git 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a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0099.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0099.json similarity index 100% rename from Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0099.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam04_json/cam04.0099.json diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam1_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam01_img/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam1_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam01_img/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam2_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam02_img/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam2_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam02_img/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam3_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam03_img/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam3_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/extrinsics/ext_cam03_img/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam1_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam01_img/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam1_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam01_img/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam2_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam02_img/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam2_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam02_img/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam3_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam03_img/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam3_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_Calibration/intrinsics/int_cam03_img/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/Config.toml similarity index 99% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/Config.toml rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/Config.toml index c31ef68..99d62ce 100644 --- a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/Config.toml +++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/Config.toml @@ -119,7 +119,7 @@ # tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py ## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) # reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 +# likelihood_error_threshold_association = 0.2 # [triangulation] diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_OpenSim/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_OpenSim/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_OpenSim/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_OpenSim/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/Config.toml similarity index 99% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/Config.toml index c31ef68..99d62ce 100644 --- a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml +++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/Config.toml @@ -119,7 +119,7 @@ # tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py ## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) # reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 +# likelihood_error_threshold_association = 0.2 # [triangulation] diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/pose/pose_cam1_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/pose/pose_cam01_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/pose/pose_cam1_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/pose/pose_cam01_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/pose/pose_cam2_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/pose/pose_cam02_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/pose/pose_cam2_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/pose/pose_cam02_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/pose/pose_cam3_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/pose/pose_cam03_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/pose/pose_cam3_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/pose/pose_cam03_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/videos/video_cam1/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/videos/video_cam01/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/videos/video_cam1/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/videos/video_cam01/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/videos/video_cam2/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/videos/video_cam02/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/videos/video_cam2/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/videos/video_cam02/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/videos/video_cam3/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/videos/video_cam03/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/videos/video_cam3/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T00_StaticTrial/videos/video_cam03/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/Config.toml similarity index 99% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/Config.toml rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/Config.toml index c31ef68..99d62ce 100644 --- a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/Config.toml +++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/Config.toml @@ -119,7 +119,7 @@ # tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py ## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) # reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 +# likelihood_error_threshold_association = 0.2 # [triangulation] diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/pose/pose_cam1_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/pose/pose_cam01_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/pose/pose_cam1_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/pose/pose_cam01_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/pose/pose_cam2_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/pose/pose_cam02_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/pose/pose_cam2_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/pose/pose_cam02_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/pose/pose_cam3_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/pose/pose_cam03_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/pose/pose_cam3_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/pose/pose_cam03_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/videos/video_cam1/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/videos/video_cam01/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/videos/video_cam1/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/videos/video_cam01/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/videos/video_cam2/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/videos/video_cam02/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/videos/video_cam2/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/videos/video_cam02/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/videos/video_cam3/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/videos/video_cam03/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/videos/video_cam3/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T01_MotionTrial1/videos/video_cam03/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/Config.toml similarity index 99% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/Config.toml index c31ef68..99d62ce 100644 --- a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml +++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/Config.toml @@ -119,7 +119,7 @@ # tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py ## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) # reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 +# likelihood_error_threshold_association = 0.2 # [triangulation] diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/pose/pose_cam1_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/pose/pose_cam01_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/pose/pose_cam1_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/pose/pose_cam01_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/pose/pose_cam2_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/pose/pose_cam02_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/pose/pose_cam2_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/pose/pose_cam02_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/pose/pose_cam3_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/pose/pose_cam03_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/pose/pose_cam3_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/pose/pose_cam03_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/videos/video_cam1/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/videos/video_cam01/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/videos/video_cam1/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/videos/video_cam01/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/videos/video_cam2/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/videos/video_cam02/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/videos/video_cam2/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/videos/video_cam02/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/videos/video_cam3/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/videos/video_cam03/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/videos/video_cam3/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant00/S01_P00_T02_MotionTrial2/videos/video_cam03/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/Config.toml new file mode 100644 index 0000000..99d62ce --- /dev/null +++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/Config.toml @@ -0,0 +1,250 @@ +############################################################################### +## PROJECT PARAMETERS ## +############################################################################### + + +# Configure your project parameters here. +# +# IMPORTANT: +# If a parameter is not found here, Pose2Sim will look for its value in the +# Config.toml file of the level above. This way, you can set global +# instructions for the Session and alter them for specific Participants or Trials. +# +# If you wish to overwrite a parameter for a specific trial or participant, +# edit its Config.toml file by uncommenting its key (e.g., [project]) +# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment +# [filtering.butterworth] and set cut_off_frequency = 10, etc. + + + +# [project] +# frame_rate = 60 # FPS +# frame_range = [] # For example [10,300], or [] for all frames +## N.B.: If you want a time range instead, use frame_range = time_range * frame_rate +## For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, +## frame_range = [0.1, 2.0]*frame_rate = [6, 120] + +# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc']. +# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial'] +## Take heart, calibration is not that complicated once you get the hang of it! + + +# [calibration] +# calibration_type = 'convert' # 'convert' or 'calculate' + + # [calibration.convert] + # 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 parameter needed + # [calibration.convert.opencap] # No parameter needed + # [calibration.convert.easymocap] # No parameter needed + # [calibration.convert.biocv] # No parameter needed + # [calibration.convert.anipose] # No parameter needed + # [calibration.convert.freemocap] # No parameter needed + + + # [calibration.calculate] + ## Camera properties, theoretically need to be calculated only once in a camera lifetime + # [calibration.calculate.intrinsics] + # overwrite_intrinsics = false # overwrite (or not) if they have already been calculated? + # show_detection_intrinsics = true # true or false (lowercase) + # intrinsics_extension = 'jpg' # any video or image extension + # extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 ) + # intrinsics_corners_nb = [4,7] + # intrinsics_square_size = 60 # mm + + ## Camera placements, need to be done before every session + # [calibration.calculate.extrinsics] + # extrinsics_method = 'scene' # 'board', 'scene', 'keypoints' + ## 'board' should be large enough to be detected when laid on the floor. Not recommended. + ## 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out. + ## 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras. + + # moving_cameras = false # Not implemented yet + # calculate_extrinsics = true # true or false (lowercase) + + # [calibration.calculate.extrinsics.board] + # show_reprojection_error = true # true or false (lowercase) + # extrinsics_extension = 'png' # any video or image extension + # extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h] + # extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle + + # [calibration.calculate.extrinsics.scene] + # show_reprojection_error = true # true or false (lowercase) + # extrinsics_extension = 'png' # any video or image extension + ## list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. + ## in m -> unlike for intrinsics, NOT in mm! + # object_coords_3d = [[-2.0, 0.3, 0.0], + # [-2.0 , 0.0, 0.0], + # [-2.0, 0.0, 0.05], + # [-2.0, -0.3 , 0.0], + # [0.0, 0.3, 0.0], + # [0.0, 0.0, 0.0], + # [0.0, 0.0, 0.05], + # [0.0, -0.3, 0.0]] + + # [calibration.calculate.extrinsics.keypoints] + ## Coming soon! + + +# [pose] +# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' +# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII, +# #With mediapipe: BLAZEPOSE. +# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. +# #With deeplabcut: CUSTOM. See example at the end of the file. +## What follows has not been implemented yet +# overwrite_pose = false +# openpose_path = '' # only checked if OpenPose is used + + +# [synchronization] +## COMING SOON! +# reset_sync = true # Recalculate synchronization even if already done +# frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion. +# cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter +## Vertical speeds (on X, Y, or Z axis, or 2D speeds) +# speed_kind = 'y' # 'x', 'y', 'z', or '2D' +# vmax = 20 # px/s +# cam1_nb = 4 +# cam2_nb = 3 +# id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7 +# weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints + + +# [personAssociation] +# single_person = true # false for multi-person analysis (not supported yet), true for only triangulating the main person in scene. +# tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py +## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) +# reproj_error_threshold_association = 20 # px +# likelihood_error_threshold_association = 0.2 + + +# [triangulation] +# reproj_error_threshold_triangulation = 15 # px +# likelihood_threshold_triangulation = 0.3 +# min_cameras_for_triangulation = 2 +# interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none +## 'none' if you don't want to interpolate missing points +# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps +# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated +# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower +# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low +# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon! + + +# [filtering] +# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed +# display_figures = true # true or false (lowercase) + + # [filtering.butterworth] + # order = 4 + # cut_off_frequency = 6 # Hz + # [filtering.kalman] + ## How much more do you trust triangulation results (measurements), than previous data (process assuming constant acceleration)? + # trust_ratio = 100 # = measurement_trust/process_trust ~= process_noise/measurement_noise + # smooth = true # should be true, unless you need real-time filtering + # [filtering.butterworth_on_speed] + # order = 4 + # cut_off_frequency = 10 # Hz + # [filtering.gaussian] + # sigma_kernel = 2 #px + # [filtering.LOESS] + # nb_values_used = 30 # = fraction of data used * nb frames + # [filtering.median] + # kernel_size = 9 + + +# [markerAugmentation] +# ## Only works on BODY_25 and BODY_25B models +# participant_height = 1.7 # m +# participant_mass = 70 # kg + + +# [opensim] +# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial'] +# # If this Config.toml file is at the Trial level, set to true or false (lowercase); +# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial']; +# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial'] +# opensim_bin_path = 'C:\OpenSim 4.4\bin' + + +## CUSTOM skeleton, if you trained your own DeepLabCut model for example. +## Make sure the node ids correspond to the column numbers of the 2D pose file, starting from zero. +## +## If you want to perform inverse kinematics, you will also need to create an OpenSim model +## and add to its markerset the location where you expect the triangulated keypoints to be detected. +## +## In this example, CUSTOM reproduces the BODY_25B skeleton (default skeletons are stored in skeletons.py). +## You can create as many custom skeletons as you want, just add them further down and rename them. +## +## Check your model hierarchy with: for pre, _, node in RenderTree(model): +## print(f'{pre}{node.name} id={node.id}') +# [pose.CUSTOM] +# name = "CHip" +# id = "None" +# [[pose.CUSTOM.children]] +# id = 12 +# name = "RHip" +# [[pose.CUSTOM.children.children]] +# id = 14 +# name = "RKnee" +# [[pose.CUSTOM.children.children.children]] +# id = 16 +# name = "RAnkle" +# [[pose.CUSTOM.children.children.children.children]] +# id = 22 +# name = "RBigToe" +# [[pose.CUSTOM.children.children.children.children.children]] +# id = 23 +# name = "RSmallToe" +# [[pose.CUSTOM.children.children.children.children]] +# id = 24 +# name = "RHeel" +# [[pose.CUSTOM.children]] +# id = 11 +# name = "LHip" +# [[pose.CUSTOM.children.children]] +# id = 13 +# name = "LKnee" +# [[pose.CUSTOM.children.children.children]] +# id = 15 +# name = "LAnkle" +# [[pose.CUSTOM.children.children.children.children]] +# id = 19 +# name = "LBigToe" +# [[pose.CUSTOM.children.children.children.children.children]] +# id = 20 +# name = "LSmallToe" +# [[pose.CUSTOM.children.children.children.children]] +# id = 21 +# name = "LHeel" +# [[pose.CUSTOM.children]] +# id = 17 +# name = "Neck" +# [[pose.CUSTOM.children.children]] +# id = 18 +# name = "Head" +# [[pose.CUSTOM.children.children.children]] +# id = 0 +# name = "Nose" +# [[pose.CUSTOM.children.children]] +# id = 6 +# name = "RShoulder" +# [[pose.CUSTOM.children.children.children]] +# id = 8 +# name = "RElbow" +# [[pose.CUSTOM.children.children.children.children]] +# id = 10 +# name = "RWrist" +# [[pose.CUSTOM.children.children]] +# id = 5 +# name = "LShoulder" +# [[pose.CUSTOM.children.children.children]] +# id = 7 +# name = "LElbow" +# [[pose.CUSTOM.children.children.children.children]] +# id = 9 +# name = "LWrist" diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_OpenSim/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_OpenSim/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_OpenSim/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_OpenSim/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/Config.toml new file mode 100644 index 0000000..99d62ce --- /dev/null +++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/Config.toml @@ -0,0 +1,250 @@ +############################################################################### +## PROJECT PARAMETERS ## +############################################################################### + + +# Configure your project parameters here. +# +# IMPORTANT: +# If a parameter is not found here, Pose2Sim will look for its value in the +# Config.toml file of the level above. This way, you can set global +# instructions for the Session and alter them for specific Participants or Trials. +# +# If you wish to overwrite a parameter for a specific trial or participant, +# edit its Config.toml file by uncommenting its key (e.g., [project]) +# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment +# [filtering.butterworth] and set cut_off_frequency = 10, etc. + + + +# [project] +# frame_rate = 60 # FPS +# frame_range = [] # For example [10,300], or [] for all frames +## N.B.: If you want a time range instead, use frame_range = time_range * frame_rate +## For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, +## frame_range = [0.1, 2.0]*frame_rate = [6, 120] + +# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc']. +# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial'] +## Take heart, calibration is not that complicated once you get the hang of it! + + +# [calibration] +# calibration_type = 'convert' # 'convert' or 'calculate' + + # [calibration.convert] + # 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 parameter needed + # [calibration.convert.opencap] # No parameter needed + # [calibration.convert.easymocap] # No parameter needed + # [calibration.convert.biocv] # No parameter needed + # [calibration.convert.anipose] # No parameter needed + # [calibration.convert.freemocap] # No parameter needed + + + # [calibration.calculate] + ## Camera properties, theoretically need to be calculated only once in a camera lifetime + # [calibration.calculate.intrinsics] + # overwrite_intrinsics = false # overwrite (or not) if they have already been calculated? + # show_detection_intrinsics = true # true or false (lowercase) + # intrinsics_extension = 'jpg' # any video or image extension + # extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 ) + # intrinsics_corners_nb = [4,7] + # intrinsics_square_size = 60 # mm + + ## Camera placements, need to be done before every session + # [calibration.calculate.extrinsics] + # extrinsics_method = 'scene' # 'board', 'scene', 'keypoints' + ## 'board' should be large enough to be detected when laid on the floor. Not recommended. + ## 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out. + ## 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras. + + # moving_cameras = false # Not implemented yet + # calculate_extrinsics = true # true or false (lowercase) + + # [calibration.calculate.extrinsics.board] + # show_reprojection_error = true # true or false (lowercase) + # extrinsics_extension = 'png' # any video or image extension + # extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h] + # extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle + + # [calibration.calculate.extrinsics.scene] + # show_reprojection_error = true # true or false (lowercase) + # extrinsics_extension = 'png' # any video or image extension + ## list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. + ## in m -> unlike for intrinsics, NOT in mm! + # object_coords_3d = [[-2.0, 0.3, 0.0], + # [-2.0 , 0.0, 0.0], + # [-2.0, 0.0, 0.05], + # [-2.0, -0.3 , 0.0], + # [0.0, 0.3, 0.0], + # [0.0, 0.0, 0.0], + # [0.0, 0.0, 0.05], + # [0.0, -0.3, 0.0]] + + # [calibration.calculate.extrinsics.keypoints] + ## Coming soon! + + +# [pose] +# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' +# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII, +# #With mediapipe: BLAZEPOSE. +# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. +# #With deeplabcut: CUSTOM. See example at the end of the file. +## What follows has not been implemented yet +# overwrite_pose = false +# openpose_path = '' # only checked if OpenPose is used + + +# [synchronization] +## COMING SOON! +# reset_sync = true # Recalculate synchronization even if already done +# frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion. +# cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter +## Vertical speeds (on X, Y, or Z axis, or 2D speeds) +# speed_kind = 'y' # 'x', 'y', 'z', or '2D' +# vmax = 20 # px/s +# cam1_nb = 4 +# cam2_nb = 3 +# id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7 +# weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints + + +# [personAssociation] +# single_person = true # false for multi-person analysis (not supported yet), true for only triangulating the main person in scene. +# tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py +## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) +# reproj_error_threshold_association = 20 # px +# likelihood_error_threshold_association = 0.2 + + +# [triangulation] +# reproj_error_threshold_triangulation = 15 # px +# likelihood_threshold_triangulation = 0.3 +# min_cameras_for_triangulation = 2 +# interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none +## 'none' if you don't want to interpolate missing points +# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps +# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated +# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower +# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low +# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon! + + +# [filtering] +# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed +# display_figures = true # true or false (lowercase) + + # [filtering.butterworth] + # order = 4 + # cut_off_frequency = 6 # Hz + # [filtering.kalman] + ## How much more do you trust triangulation results (measurements), than previous data (process assuming constant acceleration)? + # trust_ratio = 100 # = measurement_trust/process_trust ~= process_noise/measurement_noise + # smooth = true # should be true, unless you need real-time filtering + # [filtering.butterworth_on_speed] + # order = 4 + # cut_off_frequency = 10 # Hz + # [filtering.gaussian] + # sigma_kernel = 2 #px + # [filtering.LOESS] + # nb_values_used = 30 # = fraction of data used * nb frames + # [filtering.median] + # kernel_size = 9 + + +# [markerAugmentation] +# ## Only works on BODY_25 and BODY_25B models +# participant_height = 1.7 # m +# participant_mass = 70 # kg + + +# [opensim] +# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial'] +# # If this Config.toml file is at the Trial level, set to true or false (lowercase); +# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial']; +# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial'] +# opensim_bin_path = 'C:\OpenSim 4.4\bin' + + +## CUSTOM skeleton, if you trained your own DeepLabCut model for example. +## Make sure the node ids correspond to the column numbers of the 2D pose file, starting from zero. +## +## If you want to perform inverse kinematics, you will also need to create an OpenSim model +## and add to its markerset the location where you expect the triangulated keypoints to be detected. +## +## In this example, CUSTOM reproduces the BODY_25B skeleton (default skeletons are stored in skeletons.py). +## You can create as many custom skeletons as you want, just add them further down and rename them. +## +## Check your model hierarchy with: for pre, _, node in RenderTree(model): +## print(f'{pre}{node.name} id={node.id}') +# [pose.CUSTOM] +# name = "CHip" +# id = "None" +# [[pose.CUSTOM.children]] +# id = 12 +# name = "RHip" +# [[pose.CUSTOM.children.children]] +# id = 14 +# name = "RKnee" +# [[pose.CUSTOM.children.children.children]] +# id = 16 +# name = "RAnkle" +# [[pose.CUSTOM.children.children.children.children]] +# id = 22 +# name = "RBigToe" +# [[pose.CUSTOM.children.children.children.children.children]] +# id = 23 +# name = "RSmallToe" +# [[pose.CUSTOM.children.children.children.children]] +# id = 24 +# name = "RHeel" +# [[pose.CUSTOM.children]] +# id = 11 +# name = "LHip" +# [[pose.CUSTOM.children.children]] +# id = 13 +# name = "LKnee" +# [[pose.CUSTOM.children.children.children]] +# id = 15 +# name = "LAnkle" +# [[pose.CUSTOM.children.children.children.children]] +# id = 19 +# name = "LBigToe" +# [[pose.CUSTOM.children.children.children.children.children]] +# id = 20 +# name = "LSmallToe" +# [[pose.CUSTOM.children.children.children.children]] +# id = 21 +# name = "LHeel" +# [[pose.CUSTOM.children]] +# id = 17 +# name = "Neck" +# [[pose.CUSTOM.children.children]] +# id = 18 +# name = "Head" +# [[pose.CUSTOM.children.children.children]] +# id = 0 +# name = "Nose" +# [[pose.CUSTOM.children.children]] +# id = 6 +# name = "RShoulder" +# [[pose.CUSTOM.children.children.children]] +# id = 8 +# name = "RElbow" +# [[pose.CUSTOM.children.children.children.children]] +# id = 10 +# name = "RWrist" +# [[pose.CUSTOM.children.children]] +# id = 5 +# name = "LShoulder" +# [[pose.CUSTOM.children.children.children]] +# id = 7 +# name = "LElbow" +# [[pose.CUSTOM.children.children.children.children]] +# id = 9 +# name = "LWrist" diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/pose/pose_cam1_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/pose/pose_cam1_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/pose/pose_cam1_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/pose/pose_cam1_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/pose/pose_cam2_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/pose/pose_cam2_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/pose/pose_cam2_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/pose/pose_cam2_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/pose/pose_cam3_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/pose/pose_cam3_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/pose/pose_cam3_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/pose/pose_cam3_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/videos/video_cam1/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/videos/video_cam1/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/videos/video_cam1/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/videos/video_cam1/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/videos/video_cam2/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/videos/video_cam2/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/videos/video_cam2/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/videos/video_cam2/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/videos/video_cam3/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/videos/video_cam3/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/videos/video_cam3/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T00_StaticTrial/videos/video_cam3/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/Config.toml new file mode 100644 index 0000000..99d62ce --- /dev/null +++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/Config.toml @@ -0,0 +1,250 @@ +############################################################################### +## PROJECT PARAMETERS ## +############################################################################### + + +# Configure your project parameters here. +# +# IMPORTANT: +# If a parameter is not found here, Pose2Sim will look for its value in the +# Config.toml file of the level above. This way, you can set global +# instructions for the Session and alter them for specific Participants or Trials. +# +# If you wish to overwrite a parameter for a specific trial or participant, +# edit its Config.toml file by uncommenting its key (e.g., [project]) +# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment +# [filtering.butterworth] and set cut_off_frequency = 10, etc. + + + +# [project] +# frame_rate = 60 # FPS +# frame_range = [] # For example [10,300], or [] for all frames +## N.B.: If you want a time range instead, use frame_range = time_range * frame_rate +## For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, +## frame_range = [0.1, 2.0]*frame_rate = [6, 120] + +# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc']. +# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial'] +## Take heart, calibration is not that complicated once you get the hang of it! + + +# [calibration] +# calibration_type = 'convert' # 'convert' or 'calculate' + + # [calibration.convert] + # 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 parameter needed + # [calibration.convert.opencap] # No parameter needed + # [calibration.convert.easymocap] # No parameter needed + # [calibration.convert.biocv] # No parameter needed + # [calibration.convert.anipose] # No parameter needed + # [calibration.convert.freemocap] # No parameter needed + + + # [calibration.calculate] + ## Camera properties, theoretically need to be calculated only once in a camera lifetime + # [calibration.calculate.intrinsics] + # overwrite_intrinsics = false # overwrite (or not) if they have already been calculated? + # show_detection_intrinsics = true # true or false (lowercase) + # intrinsics_extension = 'jpg' # any video or image extension + # extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 ) + # intrinsics_corners_nb = [4,7] + # intrinsics_square_size = 60 # mm + + ## Camera placements, need to be done before every session + # [calibration.calculate.extrinsics] + # extrinsics_method = 'scene' # 'board', 'scene', 'keypoints' + ## 'board' should be large enough to be detected when laid on the floor. Not recommended. + ## 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out. + ## 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras. + + # moving_cameras = false # Not implemented yet + # calculate_extrinsics = true # true or false (lowercase) + + # [calibration.calculate.extrinsics.board] + # show_reprojection_error = true # true or false (lowercase) + # extrinsics_extension = 'png' # any video or image extension + # extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h] + # extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle + + # [calibration.calculate.extrinsics.scene] + # show_reprojection_error = true # true or false (lowercase) + # extrinsics_extension = 'png' # any video or image extension + ## list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. + ## in m -> unlike for intrinsics, NOT in mm! + # object_coords_3d = [[-2.0, 0.3, 0.0], + # [-2.0 , 0.0, 0.0], + # [-2.0, 0.0, 0.05], + # [-2.0, -0.3 , 0.0], + # [0.0, 0.3, 0.0], + # [0.0, 0.0, 0.0], + # [0.0, 0.0, 0.05], + # [0.0, -0.3, 0.0]] + + # [calibration.calculate.extrinsics.keypoints] + ## Coming soon! + + +# [pose] +# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' +# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII, +# #With mediapipe: BLAZEPOSE. +# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. +# #With deeplabcut: CUSTOM. See example at the end of the file. +## What follows has not been implemented yet +# overwrite_pose = false +# openpose_path = '' # only checked if OpenPose is used + + +# [synchronization] +## COMING SOON! +# reset_sync = true # Recalculate synchronization even if already done +# frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion. +# cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter +## Vertical speeds (on X, Y, or Z axis, or 2D speeds) +# speed_kind = 'y' # 'x', 'y', 'z', or '2D' +# vmax = 20 # px/s +# cam1_nb = 4 +# cam2_nb = 3 +# id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7 +# weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints + + +# [personAssociation] +# single_person = true # false for multi-person analysis (not supported yet), true for only triangulating the main person in scene. +# tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py +## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) +# reproj_error_threshold_association = 20 # px +# likelihood_error_threshold_association = 0.2 + + +# [triangulation] +# reproj_error_threshold_triangulation = 15 # px +# likelihood_threshold_triangulation = 0.3 +# min_cameras_for_triangulation = 2 +# interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none +## 'none' if you don't want to interpolate missing points +# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps +# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated +# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower +# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low +# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon! + + +# [filtering] +# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed +# display_figures = true # true or false (lowercase) + + # [filtering.butterworth] + # order = 4 + # cut_off_frequency = 6 # Hz + # [filtering.kalman] + ## How much more do you trust triangulation results (measurements), than previous data (process assuming constant acceleration)? + # trust_ratio = 100 # = measurement_trust/process_trust ~= process_noise/measurement_noise + # smooth = true # should be true, unless you need real-time filtering + # [filtering.butterworth_on_speed] + # order = 4 + # cut_off_frequency = 10 # Hz + # [filtering.gaussian] + # sigma_kernel = 2 #px + # [filtering.LOESS] + # nb_values_used = 30 # = fraction of data used * nb frames + # [filtering.median] + # kernel_size = 9 + + +# [markerAugmentation] +# ## Only works on BODY_25 and BODY_25B models +# participant_height = 1.7 # m +# participant_mass = 70 # kg + + +# [opensim] +# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial'] +# # If this Config.toml file is at the Trial level, set to true or false (lowercase); +# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial']; +# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial'] +# opensim_bin_path = 'C:\OpenSim 4.4\bin' + + +## CUSTOM skeleton, if you trained your own DeepLabCut model for example. +## Make sure the node ids correspond to the column numbers of the 2D pose file, starting from zero. +## +## If you want to perform inverse kinematics, you will also need to create an OpenSim model +## and add to its markerset the location where you expect the triangulated keypoints to be detected. +## +## In this example, CUSTOM reproduces the BODY_25B skeleton (default skeletons are stored in skeletons.py). +## You can create as many custom skeletons as you want, just add them further down and rename them. +## +## Check your model hierarchy with: for pre, _, node in RenderTree(model): +## print(f'{pre}{node.name} id={node.id}') +# [pose.CUSTOM] +# name = "CHip" +# id = "None" +# [[pose.CUSTOM.children]] +# id = 12 +# name = "RHip" +# [[pose.CUSTOM.children.children]] +# id = 14 +# name = "RKnee" +# [[pose.CUSTOM.children.children.children]] +# id = 16 +# name = "RAnkle" +# [[pose.CUSTOM.children.children.children.children]] +# id = 22 +# name = "RBigToe" +# [[pose.CUSTOM.children.children.children.children.children]] +# id = 23 +# name = "RSmallToe" +# [[pose.CUSTOM.children.children.children.children]] +# id = 24 +# name = "RHeel" +# [[pose.CUSTOM.children]] +# id = 11 +# name = "LHip" +# [[pose.CUSTOM.children.children]] +# id = 13 +# name = "LKnee" +# [[pose.CUSTOM.children.children.children]] +# id = 15 +# name = "LAnkle" +# [[pose.CUSTOM.children.children.children.children]] +# id = 19 +# name = "LBigToe" +# [[pose.CUSTOM.children.children.children.children.children]] +# id = 20 +# name = "LSmallToe" +# [[pose.CUSTOM.children.children.children.children]] +# id = 21 +# name = "LHeel" +# [[pose.CUSTOM.children]] +# id = 17 +# name = "Neck" +# [[pose.CUSTOM.children.children]] +# id = 18 +# name = "Head" +# [[pose.CUSTOM.children.children.children]] +# id = 0 +# name = "Nose" +# [[pose.CUSTOM.children.children]] +# id = 6 +# name = "RShoulder" +# [[pose.CUSTOM.children.children.children]] +# id = 8 +# name = "RElbow" +# [[pose.CUSTOM.children.children.children.children]] +# id = 10 +# name = "RWrist" +# [[pose.CUSTOM.children.children]] +# id = 5 +# name = "LShoulder" +# [[pose.CUSTOM.children.children.children]] +# id = 7 +# name = "LElbow" +# [[pose.CUSTOM.children.children.children.children]] +# id = 9 +# name = "LWrist" diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/pose/pose_cam1_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/pose/pose_cam1_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/pose/pose_cam1_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/pose/pose_cam1_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/pose/pose_cam2_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/pose/pose_cam2_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/pose/pose_cam2_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/pose/pose_cam2_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/pose/pose_cam3_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/pose/pose_cam3_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/pose/pose_cam3_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/pose/pose_cam3_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/videos/video_cam1/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/videos/video_cam1/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/videos/video_cam1/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/videos/video_cam1/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/videos/video_cam2/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/videos/video_cam2/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/videos/video_cam2/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/videos/video_cam2/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/videos/video_cam3/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/videos/video_cam3/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/videos/video_cam3/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T01_MotionTrial1/videos/video_cam3/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/Config.toml new file mode 100644 index 0000000..99d62ce --- /dev/null +++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/Config.toml @@ -0,0 +1,250 @@ +############################################################################### +## PROJECT PARAMETERS ## +############################################################################### + + +# Configure your project parameters here. +# +# IMPORTANT: +# If a parameter is not found here, Pose2Sim will look for its value in the +# Config.toml file of the level above. This way, you can set global +# instructions for the Session and alter them for specific Participants or Trials. +# +# If you wish to overwrite a parameter for a specific trial or participant, +# edit its Config.toml file by uncommenting its key (e.g., [project]) +# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment +# [filtering.butterworth] and set cut_off_frequency = 10, etc. + + + +# [project] +# frame_rate = 60 # FPS +# frame_range = [] # For example [10,300], or [] for all frames +## N.B.: If you want a time range instead, use frame_range = time_range * frame_rate +## For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, +## frame_range = [0.1, 2.0]*frame_rate = [6, 120] + +# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc']. +# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial'] +## Take heart, calibration is not that complicated once you get the hang of it! + + +# [calibration] +# calibration_type = 'convert' # 'convert' or 'calculate' + + # [calibration.convert] + # 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 parameter needed + # [calibration.convert.opencap] # No parameter needed + # [calibration.convert.easymocap] # No parameter needed + # [calibration.convert.biocv] # No parameter needed + # [calibration.convert.anipose] # No parameter needed + # [calibration.convert.freemocap] # No parameter needed + + + # [calibration.calculate] + ## Camera properties, theoretically need to be calculated only once in a camera lifetime + # [calibration.calculate.intrinsics] + # overwrite_intrinsics = false # overwrite (or not) if they have already been calculated? + # show_detection_intrinsics = true # true or false (lowercase) + # intrinsics_extension = 'jpg' # any video or image extension + # extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 ) + # intrinsics_corners_nb = [4,7] + # intrinsics_square_size = 60 # mm + + ## Camera placements, need to be done before every session + # [calibration.calculate.extrinsics] + # extrinsics_method = 'scene' # 'board', 'scene', 'keypoints' + ## 'board' should be large enough to be detected when laid on the floor. Not recommended. + ## 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out. + ## 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras. + + # moving_cameras = false # Not implemented yet + # calculate_extrinsics = true # true or false (lowercase) + + # [calibration.calculate.extrinsics.board] + # show_reprojection_error = true # true or false (lowercase) + # extrinsics_extension = 'png' # any video or image extension + # extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h] + # extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle + + # [calibration.calculate.extrinsics.scene] + # show_reprojection_error = true # true or false (lowercase) + # extrinsics_extension = 'png' # any video or image extension + ## list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. + ## in m -> unlike for intrinsics, NOT in mm! + # object_coords_3d = [[-2.0, 0.3, 0.0], + # [-2.0 , 0.0, 0.0], + # [-2.0, 0.0, 0.05], + # [-2.0, -0.3 , 0.0], + # [0.0, 0.3, 0.0], + # [0.0, 0.0, 0.0], + # [0.0, 0.0, 0.05], + # [0.0, -0.3, 0.0]] + + # [calibration.calculate.extrinsics.keypoints] + ## Coming soon! + + +# [pose] +# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' +# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII, +# #With mediapipe: BLAZEPOSE. +# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. +# #With deeplabcut: CUSTOM. See example at the end of the file. +## What follows has not been implemented yet +# overwrite_pose = false +# openpose_path = '' # only checked if OpenPose is used + + +# [synchronization] +## COMING SOON! +# reset_sync = true # Recalculate synchronization even if already done +# frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion. +# cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter +## Vertical speeds (on X, Y, or Z axis, or 2D speeds) +# speed_kind = 'y' # 'x', 'y', 'z', or '2D' +# vmax = 20 # px/s +# cam1_nb = 4 +# cam2_nb = 3 +# id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7 +# weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints + + +# [personAssociation] +# single_person = true # false for multi-person analysis (not supported yet), true for only triangulating the main person in scene. +# tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py +## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) +# reproj_error_threshold_association = 20 # px +# likelihood_error_threshold_association = 0.2 + + +# [triangulation] +# reproj_error_threshold_triangulation = 15 # px +# likelihood_threshold_triangulation = 0.3 +# min_cameras_for_triangulation = 2 +# interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none +## 'none' if you don't want to interpolate missing points +# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps +# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated +# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower +# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low +# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon! + + +# [filtering] +# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed +# display_figures = true # true or false (lowercase) + + # [filtering.butterworth] + # order = 4 + # cut_off_frequency = 6 # Hz + # [filtering.kalman] + ## How much more do you trust triangulation results (measurements), than previous data (process assuming constant acceleration)? + # trust_ratio = 100 # = measurement_trust/process_trust ~= process_noise/measurement_noise + # smooth = true # should be true, unless you need real-time filtering + # [filtering.butterworth_on_speed] + # order = 4 + # cut_off_frequency = 10 # Hz + # [filtering.gaussian] + # sigma_kernel = 2 #px + # [filtering.LOESS] + # nb_values_used = 30 # = fraction of data used * nb frames + # [filtering.median] + # kernel_size = 9 + + +# [markerAugmentation] +# ## Only works on BODY_25 and BODY_25B models +# participant_height = 1.7 # m +# participant_mass = 70 # kg + + +# [opensim] +# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial'] +# # If this Config.toml file is at the Trial level, set to true or false (lowercase); +# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial']; +# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial'] +# opensim_bin_path = 'C:\OpenSim 4.4\bin' + + +## CUSTOM skeleton, if you trained your own DeepLabCut model for example. +## Make sure the node ids correspond to the column numbers of the 2D pose file, starting from zero. +## +## If you want to perform inverse kinematics, you will also need to create an OpenSim model +## and add to its markerset the location where you expect the triangulated keypoints to be detected. +## +## In this example, CUSTOM reproduces the BODY_25B skeleton (default skeletons are stored in skeletons.py). +## You can create as many custom skeletons as you want, just add them further down and rename them. +## +## Check your model hierarchy with: for pre, _, node in RenderTree(model): +## print(f'{pre}{node.name} id={node.id}') +# [pose.CUSTOM] +# name = "CHip" +# id = "None" +# [[pose.CUSTOM.children]] +# id = 12 +# name = "RHip" +# [[pose.CUSTOM.children.children]] +# id = 14 +# name = "RKnee" +# [[pose.CUSTOM.children.children.children]] +# id = 16 +# name = "RAnkle" +# [[pose.CUSTOM.children.children.children.children]] +# id = 22 +# name = "RBigToe" +# [[pose.CUSTOM.children.children.children.children.children]] +# id = 23 +# name = "RSmallToe" +# [[pose.CUSTOM.children.children.children.children]] +# id = 24 +# name = "RHeel" +# [[pose.CUSTOM.children]] +# id = 11 +# name = "LHip" +# [[pose.CUSTOM.children.children]] +# id = 13 +# name = "LKnee" +# [[pose.CUSTOM.children.children.children]] +# id = 15 +# name = "LAnkle" +# [[pose.CUSTOM.children.children.children.children]] +# id = 19 +# name = "LBigToe" +# [[pose.CUSTOM.children.children.children.children.children]] +# id = 20 +# name = "LSmallToe" +# [[pose.CUSTOM.children.children.children.children]] +# id = 21 +# name = "LHeel" +# [[pose.CUSTOM.children]] +# id = 17 +# name = "Neck" +# [[pose.CUSTOM.children.children]] +# id = 18 +# name = "Head" +# [[pose.CUSTOM.children.children.children]] +# id = 0 +# name = "Nose" +# [[pose.CUSTOM.children.children]] +# id = 6 +# name = "RShoulder" +# [[pose.CUSTOM.children.children.children]] +# id = 8 +# name = "RElbow" +# [[pose.CUSTOM.children.children.children.children]] +# id = 10 +# name = "RWrist" +# [[pose.CUSTOM.children.children]] +# id = 5 +# name = "LShoulder" +# [[pose.CUSTOM.children.children.children]] +# id = 7 +# name = "LElbow" +# [[pose.CUSTOM.children.children.children.children]] +# id = 9 +# name = "LWrist" diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/pose/pose_cam1_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/pose/pose_cam1_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/pose/pose_cam1_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/pose/pose_cam1_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/pose/pose_cam2_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/pose/pose_cam2_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/pose/pose_cam2_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/pose/pose_cam2_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/pose/pose_cam3_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/pose/pose_cam3_json/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/pose/pose_cam3_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/pose/pose_cam3_json/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/videos/video_cam1/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/videos/video_cam1/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/videos/video_cam1/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/videos/video_cam1/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/videos/video_cam2/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/videos/video_cam2/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/videos/video_cam2/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/videos/video_cam2/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/videos/video_cam3/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/videos/video_cam3/.gitkeep similarity index 100% rename from Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/videos/video_cam3/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant01/S01_P01_T02_MotionTrial2/videos/video_cam3/.gitkeep diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/Config.toml deleted file mode 100644 index c31ef68..0000000 --- a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/Config.toml +++ /dev/null @@ -1,250 +0,0 @@ -############################################################################### -## PROJECT PARAMETERS ## -############################################################################### - - -# Configure your project parameters here. -# -# IMPORTANT: -# If a parameter is not found here, Pose2Sim will look for its value in the -# Config.toml file of the level above. This way, you can set global -# instructions for the Session and alter them for specific Participants or Trials. -# -# If you wish to overwrite a parameter for a specific trial or participant, -# edit its Config.toml file by uncommenting its key (e.g., [project]) -# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment -# [filtering.butterworth] and set cut_off_frequency = 10, etc. - - - -# [project] -# frame_rate = 60 # FPS -# frame_range = [] # For example [10,300], or [] for all frames -## N.B.: If you want a time range instead, use frame_range = time_range * frame_rate -## For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, -## frame_range = [0.1, 2.0]*frame_rate = [6, 120] - -# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc']. -# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial'] -## Take heart, calibration is not that complicated once you get the hang of it! - - -# [calibration] -# calibration_type = 'convert' # 'convert' or 'calculate' - - # [calibration.convert] - # 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 parameter needed - # [calibration.convert.opencap] # No parameter needed - # [calibration.convert.easymocap] # No parameter needed - # [calibration.convert.biocv] # No parameter needed - # [calibration.convert.anipose] # No parameter needed - # [calibration.convert.freemocap] # No parameter needed - - - # [calibration.calculate] - ## Camera properties, theoretically need to be calculated only once in a camera lifetime - # [calibration.calculate.intrinsics] - # overwrite_intrinsics = false # overwrite (or not) if they have already been calculated? - # show_detection_intrinsics = true # true or false (lowercase) - # intrinsics_extension = 'jpg' # any video or image extension - # extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 ) - # intrinsics_corners_nb = [4,7] - # intrinsics_square_size = 60 # mm - - ## Camera placements, need to be done before every session - # [calibration.calculate.extrinsics] - # extrinsics_method = 'scene' # 'board', 'scene', 'keypoints' - ## 'board' should be large enough to be detected when laid on the floor. Not recommended. - ## 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out. - ## 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras. - - # moving_cameras = false # Not implemented yet - # calculate_extrinsics = true # true or false (lowercase) - - # [calibration.calculate.extrinsics.board] - # show_reprojection_error = true # true or false (lowercase) - # extrinsics_extension = 'png' # any video or image extension - # extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h] - # extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle - - # [calibration.calculate.extrinsics.scene] - # show_reprojection_error = true # true or false (lowercase) - # extrinsics_extension = 'png' # any video or image extension - ## list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. - ## in m -> unlike for intrinsics, NOT in mm! - # object_coords_3d = [[-2.0, 0.3, 0.0], - # [-2.0 , 0.0, 0.0], - # [-2.0, 0.0, 0.05], - # [-2.0, -0.3 , 0.0], - # [0.0, 0.3, 0.0], - # [0.0, 0.0, 0.0], - # [0.0, 0.0, 0.05], - # [0.0, -0.3, 0.0]] - - # [calibration.calculate.extrinsics.keypoints] - ## Coming soon! - - -# [pose] -# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' -# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII, -# #With mediapipe: BLAZEPOSE. -# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. -# #With deeplabcut: CUSTOM. See example at the end of the file. -## What follows has not been implemented yet -# overwrite_pose = false -# openpose_path = '' # only checked if OpenPose is used - - -# [synchronization] -## COMING SOON! -# reset_sync = true # Recalculate synchronization even if already done -# frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion. -# cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter -## Vertical speeds (on X, Y, or Z axis, or 2D speeds) -# speed_kind = 'y' # 'x', 'y', 'z', or '2D' -# vmax = 20 # px/s -# cam1_nb = 4 -# cam2_nb = 3 -# id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7 -# weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints - - -# [personAssociation] -# single_person = true # false for multi-person analysis (not supported yet), true for only triangulating the main person in scene. -# tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py -## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) -# reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 - - -# [triangulation] -# reproj_error_threshold_triangulation = 15 # px -# likelihood_threshold_triangulation = 0.3 -# min_cameras_for_triangulation = 2 -# interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none -## 'none' if you don't want to interpolate missing points -# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps -# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated -# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower -# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low -# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon! - - -# [filtering] -# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed -# display_figures = true # true or false (lowercase) - - # [filtering.butterworth] - # order = 4 - # cut_off_frequency = 6 # Hz - # [filtering.kalman] - ## How much more do you trust triangulation results (measurements), than previous data (process assuming constant acceleration)? - # trust_ratio = 100 # = measurement_trust/process_trust ~= process_noise/measurement_noise - # smooth = true # should be true, unless you need real-time filtering - # [filtering.butterworth_on_speed] - # order = 4 - # cut_off_frequency = 10 # Hz - # [filtering.gaussian] - # sigma_kernel = 2 #px - # [filtering.LOESS] - # nb_values_used = 30 # = fraction of data used * nb frames - # [filtering.median] - # kernel_size = 9 - - -# [markerAugmentation] -# ## Only works on BODY_25 and BODY_25B models -# participant_height = 1.7 # m -# participant_mass = 70 # kg - - -# [opensim] -# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial'] -# # If this Config.toml file is at the Trial level, set to true or false (lowercase); -# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial']; -# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial'] -# opensim_bin_path = 'C:\OpenSim 4.4\bin' - - -## CUSTOM skeleton, if you trained your own DeepLabCut model for example. -## Make sure the node ids correspond to the column numbers of the 2D pose file, starting from zero. -## -## If you want to perform inverse kinematics, you will also need to create an OpenSim model -## and add to its markerset the location where you expect the triangulated keypoints to be detected. -## -## In this example, CUSTOM reproduces the BODY_25B skeleton (default skeletons are stored in skeletons.py). -## You can create as many custom skeletons as you want, just add them further down and rename them. -## -## Check your model hierarchy with: for pre, _, node in RenderTree(model): -## print(f'{pre}{node.name} id={node.id}') -# [pose.CUSTOM] -# name = "CHip" -# id = "None" -# [[pose.CUSTOM.children]] -# id = 12 -# name = "RHip" -# [[pose.CUSTOM.children.children]] -# id = 14 -# name = "RKnee" -# [[pose.CUSTOM.children.children.children]] -# id = 16 -# name = "RAnkle" -# [[pose.CUSTOM.children.children.children.children]] -# id = 22 -# name = "RBigToe" -# [[pose.CUSTOM.children.children.children.children.children]] -# id = 23 -# name = "RSmallToe" -# [[pose.CUSTOM.children.children.children.children]] -# id = 24 -# name = "RHeel" -# [[pose.CUSTOM.children]] -# id = 11 -# name = "LHip" -# [[pose.CUSTOM.children.children]] -# id = 13 -# name = "LKnee" -# [[pose.CUSTOM.children.children.children]] -# id = 15 -# name = "LAnkle" -# [[pose.CUSTOM.children.children.children.children]] -# id = 19 -# name = "LBigToe" -# [[pose.CUSTOM.children.children.children.children.children]] -# id = 20 -# name = "LSmallToe" -# [[pose.CUSTOM.children.children.children.children]] -# id = 21 -# name = "LHeel" -# [[pose.CUSTOM.children]] -# id = 17 -# name = "Neck" -# [[pose.CUSTOM.children.children]] -# id = 18 -# name = "Head" -# [[pose.CUSTOM.children.children.children]] -# id = 0 -# name = "Nose" -# [[pose.CUSTOM.children.children]] -# id = 6 -# name = "RShoulder" -# [[pose.CUSTOM.children.children.children]] -# id = 8 -# name = "RElbow" -# [[pose.CUSTOM.children.children.children.children]] -# id = 10 -# name = "RWrist" -# [[pose.CUSTOM.children.children]] -# id = 5 -# name = "LShoulder" -# [[pose.CUSTOM.children.children.children]] -# id = 7 -# name = "LElbow" -# [[pose.CUSTOM.children.children.children.children]] -# id = 9 -# name = "LWrist" diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/Config.toml deleted file mode 100644 index c31ef68..0000000 --- a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/Config.toml +++ /dev/null @@ -1,250 +0,0 @@ -############################################################################### -## PROJECT PARAMETERS ## -############################################################################### - - -# Configure your project parameters here. -# -# IMPORTANT: -# If a parameter is not found here, Pose2Sim will look for its value in the -# Config.toml file of the level above. This way, you can set global -# instructions for the Session and alter them for specific Participants or Trials. -# -# If you wish to overwrite a parameter for a specific trial or participant, -# edit its Config.toml file by uncommenting its key (e.g., [project]) -# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment -# [filtering.butterworth] and set cut_off_frequency = 10, etc. - - - -# [project] -# frame_rate = 60 # FPS -# frame_range = [] # For example [10,300], or [] for all frames -## N.B.: If you want a time range instead, use frame_range = time_range * frame_rate -## For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, -## frame_range = [0.1, 2.0]*frame_rate = [6, 120] - -# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc']. -# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial'] -## Take heart, calibration is not that complicated once you get the hang of it! - - -# [calibration] -# calibration_type = 'convert' # 'convert' or 'calculate' - - # [calibration.convert] - # 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 parameter needed - # [calibration.convert.opencap] # No parameter needed - # [calibration.convert.easymocap] # No parameter needed - # [calibration.convert.biocv] # No parameter needed - # [calibration.convert.anipose] # No parameter needed - # [calibration.convert.freemocap] # No parameter needed - - - # [calibration.calculate] - ## Camera properties, theoretically need to be calculated only once in a camera lifetime - # [calibration.calculate.intrinsics] - # overwrite_intrinsics = false # overwrite (or not) if they have already been calculated? - # show_detection_intrinsics = true # true or false (lowercase) - # intrinsics_extension = 'jpg' # any video or image extension - # extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 ) - # intrinsics_corners_nb = [4,7] - # intrinsics_square_size = 60 # mm - - ## Camera placements, need to be done before every session - # [calibration.calculate.extrinsics] - # extrinsics_method = 'scene' # 'board', 'scene', 'keypoints' - ## 'board' should be large enough to be detected when laid on the floor. Not recommended. - ## 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out. - ## 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras. - - # moving_cameras = false # Not implemented yet - # calculate_extrinsics = true # true or false (lowercase) - - # [calibration.calculate.extrinsics.board] - # show_reprojection_error = true # true or false (lowercase) - # extrinsics_extension = 'png' # any video or image extension - # extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h] - # extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle - - # [calibration.calculate.extrinsics.scene] - # show_reprojection_error = true # true or false (lowercase) - # extrinsics_extension = 'png' # any video or image extension - ## list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. - ## in m -> unlike for intrinsics, NOT in mm! - # object_coords_3d = [[-2.0, 0.3, 0.0], - # [-2.0 , 0.0, 0.0], - # [-2.0, 0.0, 0.05], - # [-2.0, -0.3 , 0.0], - # [0.0, 0.3, 0.0], - # [0.0, 0.0, 0.0], - # [0.0, 0.0, 0.05], - # [0.0, -0.3, 0.0]] - - # [calibration.calculate.extrinsics.keypoints] - ## Coming soon! - - -# [pose] -# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' -# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII, -# #With mediapipe: BLAZEPOSE. -# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. -# #With deeplabcut: CUSTOM. See example at the end of the file. -## What follows has not been implemented yet -# overwrite_pose = false -# openpose_path = '' # only checked if OpenPose is used - - -# [synchronization] -## COMING SOON! -# reset_sync = true # Recalculate synchronization even if already done -# frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion. -# cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter -## Vertical speeds (on X, Y, or Z axis, or 2D speeds) -# speed_kind = 'y' # 'x', 'y', 'z', or '2D' -# vmax = 20 # px/s -# cam1_nb = 4 -# cam2_nb = 3 -# id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7 -# weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints - - -# [personAssociation] -# single_person = true # false for multi-person analysis (not supported yet), true for only triangulating the main person in scene. -# tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py -## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) -# reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 - - -# [triangulation] -# reproj_error_threshold_triangulation = 15 # px -# likelihood_threshold_triangulation = 0.3 -# min_cameras_for_triangulation = 2 -# interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none -## 'none' if you don't want to interpolate missing points -# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps -# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated -# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower -# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low -# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon! - - -# [filtering] -# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed -# display_figures = true # true or false (lowercase) - - # [filtering.butterworth] - # order = 4 - # cut_off_frequency = 6 # Hz - # [filtering.kalman] - ## How much more do you trust triangulation results (measurements), than previous data (process assuming constant acceleration)? - # trust_ratio = 100 # = measurement_trust/process_trust ~= process_noise/measurement_noise - # smooth = true # should be true, unless you need real-time filtering - # [filtering.butterworth_on_speed] - # order = 4 - # cut_off_frequency = 10 # Hz - # [filtering.gaussian] - # sigma_kernel = 2 #px - # [filtering.LOESS] - # nb_values_used = 30 # = fraction of data used * nb frames - # [filtering.median] - # kernel_size = 9 - - -# [markerAugmentation] -# ## Only works on BODY_25 and BODY_25B models -# participant_height = 1.7 # m -# participant_mass = 70 # kg - - -# [opensim] -# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial'] -# # If this Config.toml file is at the Trial level, set to true or false (lowercase); -# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial']; -# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial'] -# opensim_bin_path = 'C:\OpenSim 4.4\bin' - - -## CUSTOM skeleton, if you trained your own DeepLabCut model for example. -## Make sure the node ids correspond to the column numbers of the 2D pose file, starting from zero. -## -## If you want to perform inverse kinematics, you will also need to create an OpenSim model -## and add to its markerset the location where you expect the triangulated keypoints to be detected. -## -## In this example, CUSTOM reproduces the BODY_25B skeleton (default skeletons are stored in skeletons.py). -## You can create as many custom skeletons as you want, just add them further down and rename them. -## -## Check your model hierarchy with: for pre, _, node in RenderTree(model): -## print(f'{pre}{node.name} id={node.id}') -# [pose.CUSTOM] -# name = "CHip" -# id = "None" -# [[pose.CUSTOM.children]] -# id = 12 -# name = "RHip" -# [[pose.CUSTOM.children.children]] -# id = 14 -# name = "RKnee" -# [[pose.CUSTOM.children.children.children]] -# id = 16 -# name = "RAnkle" -# [[pose.CUSTOM.children.children.children.children]] -# id = 22 -# name = "RBigToe" -# [[pose.CUSTOM.children.children.children.children.children]] -# id = 23 -# name = "RSmallToe" -# [[pose.CUSTOM.children.children.children.children]] -# id = 24 -# name = "RHeel" -# [[pose.CUSTOM.children]] -# id = 11 -# name = "LHip" -# [[pose.CUSTOM.children.children]] -# id = 13 -# name = "LKnee" -# [[pose.CUSTOM.children.children.children]] -# id = 15 -# name = "LAnkle" -# [[pose.CUSTOM.children.children.children.children]] -# id = 19 -# name = "LBigToe" -# [[pose.CUSTOM.children.children.children.children.children]] -# id = 20 -# name = "LSmallToe" -# [[pose.CUSTOM.children.children.children.children]] -# id = 21 -# name = "LHeel" -# [[pose.CUSTOM.children]] -# id = 17 -# name = "Neck" -# [[pose.CUSTOM.children.children]] -# id = 18 -# name = "Head" -# [[pose.CUSTOM.children.children.children]] -# id = 0 -# name = "Nose" -# [[pose.CUSTOM.children.children]] -# id = 6 -# name = "RShoulder" -# [[pose.CUSTOM.children.children.children]] -# id = 8 -# name = "RElbow" -# [[pose.CUSTOM.children.children.children.children]] -# id = 10 -# name = "RWrist" -# [[pose.CUSTOM.children.children]] -# id = 5 -# name = "LShoulder" -# [[pose.CUSTOM.children.children.children]] -# id = 7 -# name = "LElbow" -# [[pose.CUSTOM.children.children.children.children]] -# id = 9 -# name = "LWrist" diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/Config.toml deleted file mode 100644 index c31ef68..0000000 --- a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/Config.toml +++ /dev/null @@ -1,250 +0,0 @@ -############################################################################### -## PROJECT PARAMETERS ## -############################################################################### - - -# Configure your project parameters here. -# -# IMPORTANT: -# If a parameter is not found here, Pose2Sim will look for its value in the -# Config.toml file of the level above. This way, you can set global -# instructions for the Session and alter them for specific Participants or Trials. -# -# If you wish to overwrite a parameter for a specific trial or participant, -# edit its Config.toml file by uncommenting its key (e.g., [project]) -# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment -# [filtering.butterworth] and set cut_off_frequency = 10, etc. - - - -# [project] -# frame_rate = 60 # FPS -# frame_range = [] # For example [10,300], or [] for all frames -## N.B.: If you want a time range instead, use frame_range = time_range * frame_rate -## For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, -## frame_range = [0.1, 2.0]*frame_rate = [6, 120] - -# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc']. -# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial'] -## Take heart, calibration is not that complicated once you get the hang of it! - - -# [calibration] -# calibration_type = 'convert' # 'convert' or 'calculate' - - # [calibration.convert] - # 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 parameter needed - # [calibration.convert.opencap] # No parameter needed - # [calibration.convert.easymocap] # No parameter needed - # [calibration.convert.biocv] # No parameter needed - # [calibration.convert.anipose] # No parameter needed - # [calibration.convert.freemocap] # No parameter needed - - - # [calibration.calculate] - ## Camera properties, theoretically need to be calculated only once in a camera lifetime - # [calibration.calculate.intrinsics] - # overwrite_intrinsics = false # overwrite (or not) if they have already been calculated? - # show_detection_intrinsics = true # true or false (lowercase) - # intrinsics_extension = 'jpg' # any video or image extension - # extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 ) - # intrinsics_corners_nb = [4,7] - # intrinsics_square_size = 60 # mm - - ## Camera placements, need to be done before every session - # [calibration.calculate.extrinsics] - # extrinsics_method = 'scene' # 'board', 'scene', 'keypoints' - ## 'board' should be large enough to be detected when laid on the floor. Not recommended. - ## 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out. - ## 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras. - - # moving_cameras = false # Not implemented yet - # calculate_extrinsics = true # true or false (lowercase) - - # [calibration.calculate.extrinsics.board] - # show_reprojection_error = true # true or false (lowercase) - # extrinsics_extension = 'png' # any video or image extension - # extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h] - # extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle - - # [calibration.calculate.extrinsics.scene] - # show_reprojection_error = true # true or false (lowercase) - # extrinsics_extension = 'png' # any video or image extension - ## list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. - ## in m -> unlike for intrinsics, NOT in mm! - # object_coords_3d = [[-2.0, 0.3, 0.0], - # [-2.0 , 0.0, 0.0], - # [-2.0, 0.0, 0.05], - # [-2.0, -0.3 , 0.0], - # [0.0, 0.3, 0.0], - # [0.0, 0.0, 0.0], - # [0.0, 0.0, 0.05], - # [0.0, -0.3, 0.0]] - - # [calibration.calculate.extrinsics.keypoints] - ## Coming soon! - - -# [pose] -# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' -# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII, -# #With mediapipe: BLAZEPOSE. -# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. -# #With deeplabcut: CUSTOM. See example at the end of the file. -## What follows has not been implemented yet -# overwrite_pose = false -# openpose_path = '' # only checked if OpenPose is used - - -# [synchronization] -## COMING SOON! -# reset_sync = true # Recalculate synchronization even if already done -# frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion. -# cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter -## Vertical speeds (on X, Y, or Z axis, or 2D speeds) -# speed_kind = 'y' # 'x', 'y', 'z', or '2D' -# vmax = 20 # px/s -# cam1_nb = 4 -# cam2_nb = 3 -# id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7 -# weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints - - -# [personAssociation] -# single_person = true # false for multi-person analysis (not supported yet), true for only triangulating the main person in scene. -# tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py -## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) -# reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 - - -# [triangulation] -# reproj_error_threshold_triangulation = 15 # px -# likelihood_threshold_triangulation = 0.3 -# min_cameras_for_triangulation = 2 -# interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none -## 'none' if you don't want to interpolate missing points -# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps -# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated -# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower -# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low -# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon! - - -# [filtering] -# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed -# display_figures = true # true or false (lowercase) - - # [filtering.butterworth] - # order = 4 - # cut_off_frequency = 6 # Hz - # [filtering.kalman] - ## How much more do you trust triangulation results (measurements), than previous data (process assuming constant acceleration)? - # trust_ratio = 100 # = measurement_trust/process_trust ~= process_noise/measurement_noise - # smooth = true # should be true, unless you need real-time filtering - # [filtering.butterworth_on_speed] - # order = 4 - # cut_off_frequency = 10 # Hz - # [filtering.gaussian] - # sigma_kernel = 2 #px - # [filtering.LOESS] - # nb_values_used = 30 # = fraction of data used * nb frames - # [filtering.median] - # kernel_size = 9 - - -# [markerAugmentation] -# ## Only works on BODY_25 and BODY_25B models -# participant_height = 1.7 # m -# participant_mass = 70 # kg - - -# [opensim] -# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial'] -# # If this Config.toml file is at the Trial level, set to true or false (lowercase); -# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial']; -# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial'] -# opensim_bin_path = 'C:\OpenSim 4.4\bin' - - -## CUSTOM skeleton, if you trained your own DeepLabCut model for example. -## Make sure the node ids correspond to the column numbers of the 2D pose file, starting from zero. -## -## If you want to perform inverse kinematics, you will also need to create an OpenSim model -## and add to its markerset the location where you expect the triangulated keypoints to be detected. -## -## In this example, CUSTOM reproduces the BODY_25B skeleton (default skeletons are stored in skeletons.py). -## You can create as many custom skeletons as you want, just add them further down and rename them. -## -## Check your model hierarchy with: for pre, _, node in RenderTree(model): -## print(f'{pre}{node.name} id={node.id}') -# [pose.CUSTOM] -# name = "CHip" -# id = "None" -# [[pose.CUSTOM.children]] -# id = 12 -# name = "RHip" -# [[pose.CUSTOM.children.children]] -# id = 14 -# name = "RKnee" -# [[pose.CUSTOM.children.children.children]] -# id = 16 -# name = "RAnkle" -# [[pose.CUSTOM.children.children.children.children]] -# id = 22 -# name = "RBigToe" -# [[pose.CUSTOM.children.children.children.children.children]] -# id = 23 -# name = "RSmallToe" -# [[pose.CUSTOM.children.children.children.children]] -# id = 24 -# name = "RHeel" -# [[pose.CUSTOM.children]] -# id = 11 -# name = "LHip" -# [[pose.CUSTOM.children.children]] -# id = 13 -# name = "LKnee" -# [[pose.CUSTOM.children.children.children]] -# id = 15 -# name = "LAnkle" -# [[pose.CUSTOM.children.children.children.children]] -# id = 19 -# name = "LBigToe" -# [[pose.CUSTOM.children.children.children.children.children]] -# id = 20 -# name = "LSmallToe" -# [[pose.CUSTOM.children.children.children.children]] -# id = 21 -# name = "LHeel" -# [[pose.CUSTOM.children]] -# id = 17 -# name = "Neck" -# [[pose.CUSTOM.children.children]] -# id = 18 -# name = "Head" -# [[pose.CUSTOM.children.children.children]] -# id = 0 -# name = "Nose" -# [[pose.CUSTOM.children.children]] -# id = 6 -# name = "RShoulder" -# [[pose.CUSTOM.children.children.children]] -# id = 8 -# name = "RElbow" -# [[pose.CUSTOM.children.children.children.children]] -# id = 10 -# name = "RWrist" -# [[pose.CUSTOM.children.children]] -# id = 5 -# name = "LShoulder" -# [[pose.CUSTOM.children.children.children]] -# id = 7 -# name = "LElbow" -# [[pose.CUSTOM.children.children.children.children]] -# id = 9 -# name = "LWrist" diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/Config.toml deleted file mode 100644 index c31ef68..0000000 --- a/Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/Config.toml +++ /dev/null @@ -1,250 +0,0 @@ -############################################################################### -## PROJECT PARAMETERS ## -############################################################################### - - -# Configure your project parameters here. -# -# IMPORTANT: -# If a parameter is not found here, Pose2Sim will look for its value in the -# Config.toml file of the level above. This way, you can set global -# instructions for the Session and alter them for specific Participants or Trials. -# -# If you wish to overwrite a parameter for a specific trial or participant, -# edit its Config.toml file by uncommenting its key (e.g., [project]) -# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment -# [filtering.butterworth] and set cut_off_frequency = 10, etc. - - - -# [project] -# frame_rate = 60 # FPS -# frame_range = [] # For example [10,300], or [] for all frames -## N.B.: If you want a time range instead, use frame_range = time_range * frame_rate -## For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, -## frame_range = [0.1, 2.0]*frame_rate = [6, 120] - -# exclude_from_batch = [] # List of trials to be excluded from batch analysis, ['', 'etc']. -# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial'] -## Take heart, calibration is not that complicated once you get the hang of it! - - -# [calibration] -# calibration_type = 'convert' # 'convert' or 'calculate' - - # [calibration.convert] - # 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 parameter needed - # [calibration.convert.opencap] # No parameter needed - # [calibration.convert.easymocap] # No parameter needed - # [calibration.convert.biocv] # No parameter needed - # [calibration.convert.anipose] # No parameter needed - # [calibration.convert.freemocap] # No parameter needed - - - # [calibration.calculate] - ## Camera properties, theoretically need to be calculated only once in a camera lifetime - # [calibration.calculate.intrinsics] - # overwrite_intrinsics = false # overwrite (or not) if they have already been calculated? - # show_detection_intrinsics = true # true or false (lowercase) - # intrinsics_extension = 'jpg' # any video or image extension - # extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 ) - # intrinsics_corners_nb = [4,7] - # intrinsics_square_size = 60 # mm - - ## Camera placements, need to be done before every session - # [calibration.calculate.extrinsics] - # extrinsics_method = 'scene' # 'board', 'scene', 'keypoints' - ## 'board' should be large enough to be detected when laid on the floor. Not recommended. - ## 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out. - ## 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras. - - # moving_cameras = false # Not implemented yet - # calculate_extrinsics = true # true or false (lowercase) - - # [calibration.calculate.extrinsics.board] - # show_reprojection_error = true # true or false (lowercase) - # extrinsics_extension = 'png' # any video or image extension - # extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h] - # extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle - - # [calibration.calculate.extrinsics.scene] - # show_reprojection_error = true # true or false (lowercase) - # extrinsics_extension = 'png' # any video or image extension - ## list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. - ## in m -> unlike for intrinsics, NOT in mm! - # object_coords_3d = [[-2.0, 0.3, 0.0], - # [-2.0 , 0.0, 0.0], - # [-2.0, 0.0, 0.05], - # [-2.0, -0.3 , 0.0], - # [0.0, 0.3, 0.0], - # [0.0, 0.0, 0.0], - # [0.0, 0.0, 0.05], - # [0.0, -0.3, 0.0]] - - # [calibration.calculate.extrinsics.keypoints] - ## Coming soon! - - -# [pose] -# pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' -# pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII, -# #With mediapipe: BLAZEPOSE. -# #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. -# #With deeplabcut: CUSTOM. See example at the end of the file. -## What follows has not been implemented yet -# overwrite_pose = false -# openpose_path = '' # only checked if OpenPose is used - - -# [synchronization] -## COMING SOON! -# reset_sync = true # Recalculate synchronization even if already done -# frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion. -# cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter -## Vertical speeds (on X, Y, or Z axis, or 2D speeds) -# speed_kind = 'y' # 'x', 'y', 'z', or '2D' -# vmax = 20 # px/s -# cam1_nb = 4 -# cam2_nb = 3 -# id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7 -# weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints - - -# [personAssociation] -# single_person = true # false for multi-person analysis (not supported yet), true for only triangulating the main person in scene. -# tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py -## and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE) -# reproj_error_threshold_association = 20 # px -# likelihood_threshold_association = 0.2 - - -# [triangulation] -# reproj_error_threshold_triangulation = 15 # px -# likelihood_threshold_triangulation = 0.3 -# min_cameras_for_triangulation = 2 -# interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none -## 'none' if you don't want to interpolate missing points -# interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps -# show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated -# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower -# undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low -# make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon! - - -# [filtering] -# type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed -# display_figures = true # true or false (lowercase) - - # [filtering.butterworth] - # order = 4 - # cut_off_frequency = 6 # Hz - # [filtering.kalman] - ## How much more do you trust triangulation results (measurements), than previous data (process assuming constant acceleration)? - # trust_ratio = 100 # = measurement_trust/process_trust ~= process_noise/measurement_noise - # smooth = true # should be true, unless you need real-time filtering - # [filtering.butterworth_on_speed] - # order = 4 - # cut_off_frequency = 10 # Hz - # [filtering.gaussian] - # sigma_kernel = 2 #px - # [filtering.LOESS] - # nb_values_used = 30 # = fraction of data used * nb frames - # [filtering.median] - # kernel_size = 9 - - -# [markerAugmentation] -# ## Only works on BODY_25 and BODY_25B models -# participant_height = 1.7 # m -# participant_mass = 70 # kg - - -# [opensim] -# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial'] -# # If this Config.toml file is at the Trial level, set to true or false (lowercase); -# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial']; -# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial'] -# opensim_bin_path = 'C:\OpenSim 4.4\bin' - - -## CUSTOM skeleton, if you trained your own DeepLabCut model for example. -## Make sure the node ids correspond to the column numbers of the 2D pose file, starting from zero. -## -## If you want to perform inverse kinematics, you will also need to create an OpenSim model -## and add to its markerset the location where you expect the triangulated keypoints to be detected. -## -## In this example, CUSTOM reproduces the BODY_25B skeleton (default skeletons are stored in skeletons.py). -## You can create as many custom skeletons as you want, just add them further down and rename them. -## -## Check your model hierarchy with: for pre, _, node in RenderTree(model): -## print(f'{pre}{node.name} id={node.id}') -# [pose.CUSTOM] -# name = "CHip" -# id = "None" -# [[pose.CUSTOM.children]] -# id = 12 -# name = "RHip" -# [[pose.CUSTOM.children.children]] -# id = 14 -# name = "RKnee" -# [[pose.CUSTOM.children.children.children]] -# id = 16 -# name = "RAnkle" -# [[pose.CUSTOM.children.children.children.children]] -# id = 22 -# name = "RBigToe" -# [[pose.CUSTOM.children.children.children.children.children]] -# id = 23 -# name = "RSmallToe" -# [[pose.CUSTOM.children.children.children.children]] -# id = 24 -# name = "RHeel" -# [[pose.CUSTOM.children]] -# id = 11 -# name = "LHip" -# [[pose.CUSTOM.children.children]] -# id = 13 -# name = "LKnee" -# [[pose.CUSTOM.children.children.children]] -# id = 15 -# name = "LAnkle" -# [[pose.CUSTOM.children.children.children.children]] -# id = 19 -# name = "LBigToe" -# [[pose.CUSTOM.children.children.children.children.children]] -# id = 20 -# name = "LSmallToe" -# [[pose.CUSTOM.children.children.children.children]] -# id = 21 -# name = "LHeel" -# [[pose.CUSTOM.children]] -# id = 17 -# name = "Neck" -# [[pose.CUSTOM.children.children]] -# id = 18 -# name = "Head" -# [[pose.CUSTOM.children.children.children]] -# id = 0 -# name = "Nose" -# [[pose.CUSTOM.children.children]] -# id = 6 -# name = "RShoulder" -# [[pose.CUSTOM.children.children.children]] -# id = 8 -# name = "RElbow" -# [[pose.CUSTOM.children.children.children.children]] -# id = 10 -# name = "RWrist" -# [[pose.CUSTOM.children.children]] -# id = 5 -# name = "LShoulder" -# [[pose.CUSTOM.children.children.children]] -# id = 7 -# name = "LElbow" -# [[pose.CUSTOM.children.children.children.children]] -# id = 9 -# name = "LWrist" diff --git a/Pose2Sim/Pose2Sim.py b/Pose2Sim/Pose2Sim.py index 6cb9c1d..6bfccb9 100644 --- a/Pose2Sim/Pose2Sim.py +++ b/Pose2Sim/Pose2Sim.py @@ -100,6 +100,8 @@ def determine_level(config_dir): ''' len_paths = [len(root.split(os.sep)) for root,dirs,files in os.walk(config_dir) if 'Config.toml' in files] + if len_paths == []: + raise FileNotFoundError('Please run Pose2Sim from a Session, Participant, or Trial directory.') level = max(len_paths) - min(len_paths) + 1 return level @@ -169,6 +171,9 @@ def read_config_files(config): temp_dict.get("project").update({"project_dir":os.path.join(config_dir, os.path.relpath(root))}) if not os.path.relpath(root) in [os.path.relpath(p) for p in temp_dict.get("project").get('exclude_from_batch')]: config_dicts.append(temp_dict) + + else: + raise FileNotFoundError('Please run Pose2Sim from a Session, Participant, or Trial directory.') return level, config_dicts diff --git a/Pose2Sim/calibration.py b/Pose2Sim/calibration.py index c4926dc..500f3fa 100644 --- a/Pose2Sim/calibration.py +++ b/Pose2Sim/calibration.py @@ -31,12 +31,13 @@ ## INIT -from Pose2Sim.common import world_to_camera_persp, rotate_cam, quat2mat, euclidean_distance, natural_sort +from Pose2Sim.common import RT_qca2cv, rotate_cam, quat2mat, euclidean_distance, natural_sort, zup2yup import os import logging import pickle import numpy as np +import pandas as pd os.environ["OPENCV_LOG_LEVEL"]="FATAL" import cv2 import glob @@ -632,6 +633,22 @@ def calibrate_extrinsics(calib_dir, extrinsics_config_dict, C, S, K, D): ret, R, T = [], [], [] if extrinsics_method in ('board', 'scene'): + + + # Define 3D object points + if extrinsics_method == 'board': + extrinsics_corners_nb = extrinsics_config_dict.get('board').get('extrinsics_corners_nb') + extrinsics_square_size = extrinsics_config_dict.get('board').get('extrinsics_square_size') / 1000 # convert to meters + object_coords_3d = np.zeros((extrinsics_corners_nb[0] * extrinsics_corners_nb[1], 3), np.float32) + object_coords_3d[:, :2] = np.mgrid[0:extrinsics_corners_nb[0], 0:extrinsics_corners_nb[1]].T.reshape(-1, 2) + object_coords_3d[:, :2] = object_coords_3d[:, 0:2] * extrinsics_square_size + elif extrinsics_method == 'scene': + object_coords_3d = np.array(extrinsics_config_dict.get('scene').get('object_coords_3d'), np.float32) + + # Save reference 3D coordinates as trc + calib_output_path = os.path.join(calib_dir, f'Object_points.trc') + trc_write(object_coords_3d, calib_output_path) + for i, cam in enumerate(extrinsics_cam_listdirs_names): logging.info(f'\nCamera {cam}:') @@ -657,20 +674,12 @@ def calibrate_extrinsics(calib_dir, extrinsics_config_dict, C, S, K, D): # Find corners or label by hand if extrinsics_method == 'board': - extrinsics_corners_nb = extrinsics_config_dict.get('board').get('extrinsics_corners_nb') - extrinsics_square_size = extrinsics_config_dict.get('board').get('extrinsics_square_size') / 1000 # convert to meters - - objp = np.zeros((extrinsics_corners_nb[0] * extrinsics_corners_nb[1], 3), np.float32) - objp[:, :2] = np.mgrid[0:extrinsics_corners_nb[0], 0:extrinsics_corners_nb[1]].T.reshape(-1, 2) - objp[:, :2] = objp[:, 0:2] * extrinsics_square_size - imgp, objp_not_used = findCorners(img_vid_files[0], extrinsics_corners_nb, objp=objp, show=show_reprojection_error) + imgp, objp_not_used = findCorners(img_vid_files[0], extrinsics_corners_nb, objp=object_coords_3d, show=show_reprojection_error) if imgp == []: logging.exception('No corners found. Set "show_detection_extrinsics" to true to click corners by hand, or change extrinsic_board_type to "scene"') raise ValueError('No corners found. Set "show_detection_extrinsics" to true to click corners by hand, or change extrinsic_board_type to "scene"') elif extrinsics_method == 'scene': - object_coords_3d = np.array(extrinsics_config_dict.get('scene').get('object_coords_3d'), np.float32) - imgp, objp = imgp_objp_visualizer_clicker(img, imgp=[], objp=object_coords_3d, img_path=img_vid_files[0]) if imgp == []: logging.exception('No points clicked (or fewer than 6). Press \'C\' when the image is displayed, and then click on the image points corresponding to the \'object_coords_3d\' you measured and wrote down in the Config.toml file.') @@ -727,7 +736,7 @@ def calibrate_extrinsics(calib_dir, extrinsics_config_dict, C, S, K, D): ret.append(rms_px) R.append(r) T.append(t) - + elif extrinsics_method == 'keypoints': raise NotImplementedError('This has not been integrated yet.') @@ -1136,6 +1145,45 @@ def extract_frames(video_path, extract_every_N_sec=1, overwrite_extraction=False break +def trc_write(object_coords_3d, trc_path): + ''' + Make Opensim compatible trc file from a dataframe with 3D coordinates + + INPUT: + - object_coords_3d: list of 3D point lists + - trc_path: output path of the trc file + + OUTPUT: + - trc file with 2 frames of the same 3D points + ''' + + #Header + DataRate = CameraRate = OrigDataRate = 1 + NumFrames = 2 + NumMarkers = len(object_coords_3d) + keypoints_names = np.arange(NumMarkers) + header_trc = ['PathFileType\t4\t(X/Y/Z)\t' + os.path.basename(trc_path), + 'DataRate\tCameraRate\tNumFrames\tNumMarkers\tUnits\tOrigDataRate\tOrigDataStartFrame\tOrigNumFrames', + '\t'.join(map(str,[DataRate, CameraRate, NumFrames, NumMarkers, 'm', OrigDataRate, NumFrames])), + 'Frame#\tTime\t' + '\t\t\t'.join(str(k) for k in keypoints_names) + '\t\t', + '\t\t'+'\t'.join([f'X{i+1}\tY{i+1}\tZ{i+1}' for i in range(NumMarkers)])] + + # Zup to Yup coordinate system + object_coords_3d = pd.DataFrame([np.array(object_coords_3d).flatten(), np.array(object_coords_3d).flatten()]) + object_coords_3d = zup2yup(object_coords_3d) + + #Add Frame# and Time columns + object_coords_3d.index = np.array(range(0, NumFrames)) + 1 + object_coords_3d.insert(0, 't', object_coords_3d.index / DataRate) + + #Write file + with open(trc_path, 'w') as trc_o: + [trc_o.write(line+'\n') for line in header_trc] + object_coords_3d.to_csv(trc_o, sep='\t', index=True, header=None, lineterminator='\n') + + return trc_path + + def toml_write(calib_path, C, S, D, K, R, T): ''' Writes calibration parameters to a .toml file @@ -1241,7 +1289,7 @@ def calibrate_cams_all(config): list_dir_noext = sorted([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 - elif convert_filetype=='biocv' or convert_filetype=='biocv': # no conversion needed, skips this stage + elif convert_filetype=='anipose' or convert_filetype=='freemocap': # no conversion needed, skips this stage logging.info(f'\n--> No conversion needed from AniPose nor from FreeMocap. Calibration skipped.\n') return else: diff --git a/Pose2Sim/common.py b/Pose2Sim/common.py index 5cc8809..eea2385 100644 --- a/Pose2Sim/common.py +++ b/Pose2Sim/common.py @@ -99,7 +99,7 @@ def computeP(calib_file, undistort=False): T = np.array(calib[cam]['translation']) H = np.block([[R,T.reshape(3,1)], [np.zeros(3), 1 ]]) - P.append(Kh @ H) + P.append(Kh.dot(H)) return P @@ -149,8 +149,8 @@ def reprojection(P_all, Q): x_calc, y_calc = [], [] for c in range(len(P_all)): P_cam = P_all[c] - x_calc.append(P_cam[0] @ Q / (P_cam[2] @ Q)) - y_calc.append(P_cam[1] @ Q / (P_cam[2] @ Q)) + x_calc.append(P_cam[0].dot(Q) / P_cam[2].dot(Q)) + y_calc.append(P_cam[1].dot(Q) / P_cam[2].dot(Q)) return x_calc, y_calc @@ -177,10 +177,10 @@ def euclidean_distance(q1, q2): return euc_dist -def world_to_camera_persp(r, t): +def RT_qca2cv(r, t): ''' Converts rotation R and translation T - from Qualisys world centered perspective + from Qualisys object centered perspective to OpenCV camera centered perspective and inversely. @@ -188,7 +188,7 @@ def world_to_camera_persp(r, t): ''' r = r.T - t = - r @ t + t = - r.dot(t) return r, t @@ -208,10 +208,10 @@ def rotate_cam(r, t, ang_x=0, ang_y=0, ang_z=0): r_ax_x = np.array([1,0,0, 0,np.cos(ang_x),-np.sin(ang_x), 0,np.sin(ang_x),np.cos(ang_x)]).reshape(3,3) r_ax_y = np.array([np.cos(ang_y),0,np.sin(ang_y), 0,1,0, -np.sin(ang_y),0,np.cos(ang_y)]).reshape(3,3) r_ax_z = np.array([np.cos(ang_z),-np.sin(ang_z),0, np.sin(ang_z),np.cos(ang_z),0, 0,0,1]).reshape(3,3) - r_ax = r_ax_z @ r_ax_y @ r_ax_x + r_ax = r_ax_z.dot(r_ax_y).dot(r_ax_x) r_ax_h = np.block([[r_ax,np.zeros(3).reshape(3,1)], [np.zeros(3), 1]]) - r_ax_h__rt_h = r_ax_h @ rt_h + r_ax_h__rt_h = r_ax_h.dot(rt_h) r = r_ax_h__rt_h[:3,:3] t = r_ax_h__rt_h[:3,3] @@ -292,6 +292,27 @@ def natural_sort(list): return sorted(list, key=alphanum_key) +def zup2yup(Q): + ''' + Turns Z-up system coordinates into Y-up coordinates + + INPUT: + - Q: pandas dataframe + N 3D points as columns, ie 3*N columns in Z-up system coordinates + and frame number as rows + + OUTPUT: + - Q: pandas dataframe with N 3D points in Y-up system coordinates + ''' + + # X->Y, Y->Z, Z->X + cols = list(Q.columns) + cols = np.array([[cols[i*3+1],cols[i*3+2],cols[i*3]] for i in range(int(len(cols)/3))]).flatten() + Q = Q[cols] + + return Q + + ## CLASSES class plotWindow(): ''' diff --git a/Pose2Sim/triangulation.py b/Pose2Sim/triangulation.py index bf47161..7c31841 100644 --- a/Pose2Sim/triangulation.py +++ b/Pose2Sim/triangulation.py @@ -50,7 +50,7 @@ from anytree.importer import DictImporter import logging from Pose2Sim.common import retrieve_calib_params, computeP, weighted_triangulation, \ - reprojection, euclidean_distance, natural_sort + reprojection, euclidean_distance, natural_sort, zup2yup from Pose2Sim.skeletons import * @@ -66,27 +66,6 @@ __status__ = "Development" ## FUNCTIONS -def zup2yup(Q): - ''' - Turns Z-up system coordinates into Y-up coordinates - - INPUT: - - Q: pandas dataframe - N 3D points as columns, ie 3*N columns in Z-up system coordinates - and frame number as rows - - OUTPUT: - - Q: pandas dataframe with N 3D points in Y-up system coordinates - ''' - - # X->Y, Y->Z, Z->X - cols = list(Q.columns) - cols = np.array([[cols[i*3+1],cols[i*3+2],cols[i*3]] for i in range(int(len(cols)/3))]).flatten() - Q = Q[cols] - - return Q - - def interpolate_zeros_nans(col, *args): ''' Interpolate missing points (of value zero), @@ -388,9 +367,16 @@ def triangulation_from_best_cameras(config, coords_2D_kpt, coords_2D_kpt_swapped # print('error ', error) # Choosing best triangulation (with min reprojection error) + # print('\n', error) + # print('len(error) ', len(error)) + # print('len(x_calc_filt) ', len(x_calc_filt)) + # print('len(likelihood_files_filt) ', len(likelihood_files_filt)) + # print('len(id_cams_off_tot) ', len(id_cams_off_tot)) + # print('min error ', np.nanmin(error)) + # print('argmin error ', np.nanargmin(error)) error_min = np.nanmin(error) # print(error_min) - best_cams = np.argmin(error) + best_cams = np.nanargmin(error) nb_cams_excluded = nb_cams_excluded_filt[best_cams] Q = Q_filt[best_cams][:-1] @@ -398,6 +384,7 @@ def triangulation_from_best_cameras(config, coords_2D_kpt, coords_2D_kpt_swapped # Swap left and right sides if reprojection error still too high if handle_LR_swap and error_min > error_threshold_triangulation: + print('handle') n_cams_swapped = 1 error_off_swap_min = error_min while error_off_swap_min > error_threshold_triangulation and n_cams_swapped < (n_cams - nb_cams_off_tot) / 2: # more than half of the cameras switched: may triangulate twice the same side @@ -469,10 +456,19 @@ def triangulation_from_best_cameras(config, coords_2D_kpt, coords_2D_kpt_swapped Q = Q_best # print(error_min) + nb_cams_off += 1 # Index of excluded cams for this keypoint + # print('Loop ended') + if 'best_cams' in locals(): + # print(id_cams_off_tot) + # print('len(id_cams_off_tot) ', len(id_cams_off_tot)) + # print('id_cams_off_tot ', id_cams_off_tot) + id_excluded_cams = id_cams_off_tot[best_cams] + # print('id_excluded_cams ', id_excluded_cams) + id_excluded_cams = id_cams_off_tot[best_cams] else: id_excluded_cams = list(range(n_cams)) @@ -610,9 +606,12 @@ def triangulate_all(config): frames_nb = f_range[1]-f_range[0] n_cams = len(json_dirs_names) + Q_tot, error_tot, nb_cams_excluded_tot,id_excluded_cams_tot = [], [], [], [] for f in tqdm(range(*f_range)): # Get x,y,likelihood values from files + + json_tracked_files_f = [json_tracked_files[c][f] for c in range(n_cams)] # print(json_tracked_files_f) x_files, y_files, likelihood_files = extract_files_frame_f(json_tracked_files_f, keypoints_ids) @@ -634,6 +633,7 @@ def triangulate_all(config): Q, error, nb_cams_excluded, id_excluded_cams = [], [], [], [] for keypoint_idx in keypoints_idx: # Triangulate cameras with min reprojection error + # print('\n', keypoints_names[keypoint_idx]) coords_2D_kpt = np.array( (x_files[:, keypoint_idx], y_files[:, keypoint_idx], likelihood_files[:, keypoint_idx]) ) coords_2D_kpt_swapped = np.array(( x_files[:, keypoints_idx_swapped[keypoint_idx]], y_files[:, keypoints_idx_swapped[keypoint_idx]], likelihood_files[:, keypoints_idx_swapped[keypoint_idx]] ))