Merge branch 'draft-0.4' of https://github.com/perfanalytics/pose2sim into draft-0.4

Pose2Sim/Demo/User/Config.toml

@@ -15,7 +15,7 @@ pose_folder_name = 'pose'
 pose_json_folder_extension = 'json'
 pose_img_folder_extension = 'img'
 poseAssociated_folder_name = 'pose-associated'
-pose3d_folder_name = 'triangulation'
+pose3d_folder_name = 'pose-3d'
 opensim_folder_name = 'opensim'
 
 
@@ -26,7 +26,7 @@ pose_model = 'BODY_25B' #CUSTOM, BODY_25B, BODY_25, BODY_135, BLAZEPOSE, HALPE_2
 
 
 [calibration]
-calibration_type = 'convert' # 'convert' or 'calculate'
+calibration_type = 'calculate' # 'convert' or 'calculate'
 
    [calibration.convert]
    convert_from = 'qualisys' # 'qualisys', 'optitrack', or 'vicon'
@@ -34,40 +34,40 @@ calibration_type = 'convert' # 'convert' or 'calculate'
       binning_factor = 1 # Usually 1, except when filming in 540p where it usually is 2
   
 
-   [calibration.calculate] # coming later: 'points'
+   [calibration.calculate] 
    calculate_method = 'board' # 'board' or 'points'
       
       [calibration.calculate.board.intrinsics] # camera properties, only needs to be done once
       intrinsics_board_type = 'checkerboard' # 'checkerboard' ('charucoboard' not supported yet)
-
       overwrite_intrinsics = false # overwrite (or not) if they have already been calculated?
-     intrinsics_extension = 'avi' # any video or image extension
+      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 )
 
-     show_detection_intrinsics = true # true or false (lowercase). Close window to proceed to next detection
+      intrinsics_corners_nb = [4,7] 
-     intrinsics_corners_nb = [6,9] 
+      intrinsics_square_size = 60 # mm
-     intrinsics_square_size = 80 # mm
+      intrinsics_marker_size = 40 # mm # only checked if charucoboard
-     intrinsics_marker_size = 60 # mm # only checked if charucoboard
       intrinsics_aruco_dict = 'DICT_6X6_250' # only checked if charucoboard # see https://docs.opencv.org/3.4/dc/df7/dictionary_8hpp.html
    
-
       [calibration.calculate.board.extrinsics] # camera placement, needs to be done every time
-     extrinsics_board_type = 'checkerboard' # 'checkerboard', 'scene'  ('charucoboard' not supported yet)
+      extrinsics_board_type = 'scene' # 'checkerboard', 'scene'  ('charucoboard' not supported yet)
       # 'board' should be large enough to be detected when laid on the floor. 
       # 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out
+      calculate_extrinsics = true # true or false (lowercase)
+      show_reprojection_error = true # true or false (lowercase)
       
-     calculate_extrinsic = true # true or false (lowercase)
+      extrinsics_extension = 'png' # any video or image extension
-     extrinsics_extension = 'avi' # any video or image extension
       
       # if extrinsics_board_type = 'checkerboard' or 'charucoboard'
-     extrinsics_corners_nb = [6,9] # [H,W] rather than [w,h]
+      extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h]
-     extrinsics_square_size = 80 # mm # [h,w] if square is actually a rectangle
+      extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle
-     extrinsics_marker_size = 60 # mm # only checked if 'charucoboard' (not supported yet)
+      extrinsics_marker_size = 40 # mm # only checked if 'charucoboard' (not supported yet)
       extrinsics_aruco_dict = 'DICT_6X6_250' # only checked if 'charucoboard' # see https://docs.opencv.org/3.4/dc/df7/dictionary_8hpp.html
       
       # if extrinsics_board_type = 'scene'
-     # list of 3D coordinates to be manually labelled on images. Can also be 2 dimensional.
+      # list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. # in m
-     object_coords_3d = [[0,0,0],[10,0,0],[10,0,0],[10,10,0],[5,5,5]] 
+      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]] # in meters -> Not in mm! <-
       
   
       [calibration.calculate.points]
@@ -91,15 +91,17 @@ show_interp_indices = false # true or false (lowercase). For each keypoint, retu
 
 
 [filtering]
-type = 'butterworth' # butterworth, butterworth_on_speed, gaussian, LOESS, median
+type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed
 display_figures = true # true or false (lowercase)
 
    [filtering.butterworth]
-   type = 'low'
    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]
-   type = 'low'
    order = 4 
    cut_off_frequency = 10 # Hz
    [filtering.gaussian]

Pose2Sim/Demo/calibration/Calib.qca.txt

@@ -2,7 +2,7 @@
 <calibration created="sometimes ago" longArmEnd="none" longArmMiddle="none" maximumFrames="none" qtm-version="none" shortArmEnd="none" source="calibration_qca_rotated.qca.txt" type="regular" wandLength="none">
   <results min-max-diff="0." std-dev="0."/>
   <cameras>
-    <camera active="1" avg-residual="0.402000" model="none" point-count="999999999" serial="cam01" viewrotation="0">
+    <camera active="1" avg-residual="0.402000" model="none" point-count="999999999" serial="cam_01" viewrotation="0">
       <fov_marker bottom="1919" left="0" right="1087" top="0"/>
       <fov_marker_max bottom="1919" left="0" right="1087" top="0"/>
       <fov_video bottom="1919" left="0" right="1087" top="0"/>
@@ -10,7 +10,7 @@
       <transform r11="0.5536380477336265" r12="0.8046719867383512" r13="0.2144479094331626" r21="-0.4345300743838753" r22="0.05946489349975602" r23="0.8986921279821063" r31="0.7104002579937896" r32="-0.5907342212870501" r33="0.3825762057979294" x="1460.2323709212087" y="-1909.1590482454608" z="1896.5058524092062"/>
       <intrinsic centerPointU="34110.316406" centerPointV="60680.792969" focalLengthU="107599.671875" focalLengthV="107588.828125" focallength="9.314096596679686" radialDistortion1="-0.046183" radialDistortion2="0.139983" radialDistortion3="0.000000" sensorMaxU="69568" sensorMaxV="122816" sensorMinU="0.000000" sensorMinV="0.000000" skew="0.000000" tangentalDistortion1="0.000608" tangentalDistortion2="0.00069"/>
     </camera>
-    <camera active="1" avg-residual="0.444749" model="none" point-count="999999999" serial="cam02" viewrotation="0">
+    <camera active="1" avg-residual="0.444749" model="none" point-count="999999999" serial="cam_02" viewrotation="0">
       <fov_marker bottom="1919" left="0" right="1087" top="0"/>
       <fov_marker_max bottom="1919" left="0" right="1087" top="0"/>
       <fov_video bottom="1919" left="0" right="1087" top="0"/>
@@ -18,7 +18,7 @@
       <transform r11="-0.1966832217091926" r12="0.979523227309506" r13="-0.043011131806342306" r21="-0.31478107085300017" r22="-0.02153908797812718" r23="0.9489198834051846" r31="0.9285626460991909" r32="0.20017570994064315" r33="0.3125717476340885" x="2582.0136248568124" y="706.5662881637625" z="1690.9818366061595"/>
       <intrinsic centerPointU="34207.652344" centerPointV="61646.457031" focalLengthU="107118.695313" focalLengthV="107123.023438" focallength="9.272462063031563" radialDistortion1="-0.047847" radialDistortion2="0.136786" radialDistortion3="0.000000" sensorMaxU="69568" sensorMaxV="122816" sensorMinU="0.000000" sensorMinV="0.000000" skew="0.000000" tangentalDistortion1="0.000972" tangentalDistortion2="0.000291"/>
     </camera>
-    <camera active="1" avg-residual="0.450323" model="none" point-count="999999999" serial="cam03" viewrotation="0">
+    <camera active="1" avg-residual="0.450323" model="none" point-count="999999999" serial="cam_03" viewrotation="0">
       <fov_marker bottom="1919" left="0" right="1087" top="0"/>
       <fov_marker_max bottom="1919" left="0" right="1087" top="0"/>
       <fov_video bottom="1919" left="0" right="1087" top="0"/>
@@ -26,7 +26,7 @@
       <transform r11="-0.740641130147863" r12="-0.6704153360235378" r13="-0.044654154988568895" r21="0.25251118212268814" r22="-0.3393170985114385" r23="0.9061467925015139" r31="-0.6226466246887545" r32="0.6598539110153292" r33="0.4205995683324882" x="-3216.86586729648" y="2231.1786368869416" z="2088.19103027083"/>
       <intrinsic centerPointU="32845.335938" centerPointV="61120.328125" focalLengthU="107622.296875" focalLengthV="107616.632813" focallength="9.316055073242188" radialDistortion1="-0.046705" radialDistortion2="0.137622" radialDistortion3="0.000000" sensorMaxU="69568" sensorMaxV="122816" sensorMinU="0.000000" sensorMinV="0.000000" skew="0.000000" tangentalDistortion1="-0.000542" tangentalDistortion2="-0.000517"/>
     </camera>
-    <camera active="1" avg-residual="0.504772" model="none" point-count="999999999" serial="cam04" viewrotation="0">
+    <camera active="1" avg-residual="0.504772" model="none" point-count="999999999" serial="cam_04" viewrotation="0">
       <fov_marker bottom="1919" left="0" right="1087" top="0"/>
       <fov_marker_max bottom="1919" left="0" right="1087" top="0"/>
       <fov_video bottom="1919" left="0" right="1087" top="0"/>

Pose2Sim/Demo/calibration/Calib_intcheckerboard_extrandom-old.toml

@@ -1,30 +0,0 @@
-[cam_1]
-name = "cam_01"
-size = [ 1920.0, 1080.0]
-matrix = [ [ 1203.246243533484, 0.0, 959.5], [ 0.0, 1198.3711959207449, 539.5], [ 0.0, 0.0, 1.0]]
-distortions = [ -0.044787602246347216, -0.5273833010005556, 0.009327766682582903, 0.00034371130233083687]
-rotation = [ 0, 0, 0]
-translation = [ 0, 0, 0]
-fisheye = false
-
-[cam_2]
-name = "cam_02"
-size = [ 1920.0, 1080.0]
-matrix = [ [ 1201.3535871331092, 0.0, 959.5], [ 0.0, 1296.9584035037935, 539.5], [ 0.0, 0.0, 1.0]]
-distortions = [ 0.016997873879159856, 0.15076005731825853, -0.07849748162325841, 0.0031187917923049886]
-rotation = [ 0, 0, 0]
-translation = [ 0, 0, 0]
-fisheye = false
-
-[cam_3]
-name = "cam_03"
-size = [ 1920.0, 1080.0]
-matrix = [ [ 1375.7450722547337, 0.0, 959.5], [ 0.0, 1367.6433832166495, 539.5], [ 0.0, 0.0, 1.0]]
-distortions = [ -0.008547555195961013, -0.1321001559843561, 0.002017158533123475, 0.0033830082027901435]
-rotation = [ 0, 0, 0]
-translation = [ 0, 0, 0]
-fisheye = false
-
-[metadata]
-adjusted = false
-error = 0.0

Pose2Sim/Demo/calibration/Calib_intcheckerboard_extrandom.toml

@@ -1,30 +0,0 @@
-[cam_1]
-name = "cam_01"
-size = [ 1920.0, 1080.0]
-matrix = [ [ 1206.3039773711387, 0.0, 959.5], [ 0.0, 1201.3900241712472, 539.5], [ 0.0, 0.0, 1.0]]
-distortions = [ -0.048195523248209984, -0.49433115008284967, 0.009146097668361275, 0.00023449575614186346]
-rotation = [ 0, 0, 0]
-translation = [ 0, 0, 0]
-fisheye = false
-
-[cam_2]
-name = "cam_02"
-size = [ 1920.0, 1080.0]
-matrix = [ [ 1201.3535871331092, 0.0, 959.5], [ 0.0, 1296.9584035037935, 539.5], [ 0.0, 0.0, 1.0]]
-distortions = [ 0.016997873879159856, 0.15076005731825853, -0.07849748162325841, 0.0031187917923049886]
-rotation = [ 0, 0, 0]
-translation = [ 0, 0, 0]
-fisheye = false
-
-[cam_3]
-name = "cam_03"
-size = [ 1920.0, 1080.0]
-matrix = [ [ 1334.9930217175306, 0.0, 959.5], [ 0.0, 1527.484911404606, 539.5], [ 0.0, 0.0, 1.0]]
-distortions = [ 0.03903616767043438, -0.21066010320288212, -0.024219751825038247, 0.004221082947531837]
-rotation = [ 0, 0, 0]
-translation = [ 0, 0, 0]
-fisheye = false
-
-[metadata]
-adjusted = false
-error = 0.0

Pose2Sim/Demo/calibration/Calib_intcheckerboard_extscene.toml

@@ -0,0 +1,39 @@
+[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 = [ [1.70179346], [1.04839803], [-0.40602443]]
+translation = [ [0.31962238], [0.93995713], [2.97508412]]
+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 = [ [1.35902244], [1.60141928], [-1.18177902]]
+translation = [ [-0.12599186], [0.74502948], [3.17221429]]
+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 = [ [0.81816165], [-2.22184308], [1.4608978]]
+translation = [ [-0.76301979], [0.34503189], [4.43845847]]
+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 = [ [1.4245729], [-1.39512301], [0.45721172]]
+translation = [ [0.48659282], [0.02675454], [4.33496911]]
+fisheye = false
+
+[metadata]
+adjusted = false
+error = 0.0

Pose2Sim/Demo/calibration/Calib_intcheckerboard_extzeros.toml.old

@@ -0,0 +1,39 @@
+[cam_1]
+name = "cam_01"
+size = [ 1088.0, 1920.0]
+matrix = [ [ 1687.6396622414502, 0.0, 543.5], [ 0.0, 1686.6625452424132, 959.5], [ 0.0, 0.0, 1.0]]
+distortions = [ -0.05054882348909584, 0.1576374662929963, 0.002210439026715273, -0.002164250840100675]
+rotation = [ 0, 0, 0]
+translation = [ 0, 0, 0]
+fisheye = false
+
+[cam_2]
+name = "cam_02"
+size = [ 1088.0, 1920.0]
+matrix = [ [ 1687.859605173682, 0.0, 543.5], [ 0.0, 1685.4371774565182, 959.5], [ 0.0, 0.0, 1.0]]
+distortions = [ -0.03518095956993663, 0.037170387967130306, 0.0017983248726869015, -0.0018747264134721386]
+rotation = [ 0, 0, 0]
+translation = [ 0, 0, 0]
+fisheye = false
+
+[cam_3]
+name = "cam_03"
+size = [ 1088.0, 1920.0]
+matrix = [ [ 1680.286039024573, 0.0, 543.5], [ 0.0, 1681.1761700950424, 959.5], [ 0.0, 0.0, 1.0]]
+distortions = [ -0.030304789365317657, 0.04613237843981006, 0.004618104732402956, -0.001684974310757026]
+rotation = [ 0, 0, 0]
+translation = [ 0, 0, 0]
+fisheye = false
+
+[cam_4]
+name = "cam_04"
+size = [ 1088.0, 1920.0]
+matrix = [ [ 1689.483288223434, 0.0, 543.5], [ 0.0, 1688.5630322142706, 959.5], [ 0.0, 0.0, 1.0]]
+distortions = [ -0.04369424846208241, 0.12212413289800295, 0.0017367557051414114, -0.0018985222378279064]
+rotation = [ 0, 0, 0]
+translation = [ 0, 0, 0]
+fisheye = false
+
+[metadata]
+adjusted = false
+error = 0.0

Pose2Sim/Demo/calibration/Calib_qualisys.toml

@@ -1,5 +1,5 @@
-[cam_1]
+[cam_01]
-name = "cam01"
+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]
@@ -7,31 +7,31 @@ rotation = [ 1.6882754799999993, 1.0483220499999997, -0.41955852000000016]
 translation = [ 0.3211048899999996, 0.9563320600000009, 2.8907130499999996]
 fisheye = false
 
-[cam_2]
+[cam_02]
-name = "cam02"
+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 = [ -0.1115282900000002, 0.7766184800000001, 3.0675519599999994]
+translation = [ -0.11152829000000017, 0.7766184800000001, 3.0675519599999994]
 fisheye = false
 
-[cam_3]
+[cam_03]
-name = "cam03"
+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 = [ -0.7934803899999995, 0.32283594000000126, 4.353514870000001]
+translation = [ -0.7934803899999996, 0.32283594000000126, 4.353514870000001]
 fisheye = false
 
-[cam_4]
+[cam_04]
-name = "cam04"
+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 = [ 0.5030217200000006, 0.04894934000000085, 4.406564460000002]
+translation = [ 0.5030217200000007, 0.04894934000000083, 4.406564460000002]
 fisheye = false
 
 [metadata]

Pose2Sim/Demo/calibration/Calib_qualisys.toml.old

@@ -0,0 +1,39 @@
+[cam_1]
+name = "cam01"
+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_2]
+name = "cam02"
+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_3]
+name = "cam03"
+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_4]
+name = "cam04"
+size = [ 1088.0, 1920.0]
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+translation = [ 0.5030217200000007, 0.04894934000000083, 4.406564460000002]
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+[metadata]
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+error = 0.0