Operating system: Windows 10 pro (X64)
Slicer version: 5.6.2
Expected behavior: I hope to be able to automatically place landmarks in 3D meshes generated by photogrammetry, employing templates made with microtomography.
Actual behavior: I attach the screenshots of the errors and warnings.
Please copy and paste the errors. Screenshots are too blurry to read.
Hello, thanks for reply. I´m sorry about screenshots quality, it´s were a lot notifications.
Switch to module: “ALPACA”
ReadDataInternal ((unknown)): File D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Bases de Datos/Especimenes/3D/FotogrametrÍa/Ingroup/Craneos/Chve\Chve_MACN-Ma_14821_Cr.ply does not contain coordinate system information. Assuming LPS.
“Model” Reader has successfully read the file “D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Bases de Datos/Especimenes/3D/FotogrametrÍa/Ingroup/Craneos/Chve\Chve_MACN-Ma_14821_Cr.ply” “[0.12s]”
ReadDataInternal ((unknown)): File D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/Mesh Templates/Chve_MACN-Ma_35.337_Cr.ply does not contain coordinate system information. Assuming LPS.
“Model” Reader has successfully read the file “D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/Mesh Templates/Chve_MACN-Ma_35.337_Cr.ply” “[0.93s]”
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 83.40928102753698 90.81990677220223
Voxel Size is 1.5165323823188541
Scaling factor is 1
There are no errors in the log you shared. ALPACA seems to be working (or at least no generating any errors up to that point). Why do you think there is an error?
Can you share your data?
So far I have not obtained the output with the coordinates of landmarks in the target specimens
These are errors at other set of specimens:
GetArrayItemsStringProperty: markups property is not an array
Traceback (most recent call last):
File “C:/ProgramData/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py”, line 951, in onApplyLandmarkMulti
logic.runLandmarkMultiprocess(
File “C:/ProgramData/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py”, line 1561, in runLandmarkMultiprocess
array = self.pairwiseAlignment(
File “C:/ProgramData/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py”, line 1618, in pairwiseAlignment
sourceLandmarks, sourceLMNode = self.loadAndScaleFiducials(
File “C:/ProgramData/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py”, line 2866, in loadAndScaleFiducials
sourceLandmarkNode = slicer.util.loadMarkups(fiducial)
File “C:\ProgramData[slicer.org](http://slicer.org)\Slicer 5.6.2\bin\Python\slicer\util.py”, line 863, in loadMarkups
return loadNodeFromFile(filename, “MarkupsFile”)
File “C:\ProgramData[slicer.org](http://slicer.org)\Slicer 5.6.2\bin\Python\slicer\util.py”, line 734, in loadNodeFromFile
raise RuntimeError(errorMessage)
RuntimeError: Failed to load node from file: D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/.mrkps.json Templates/Dasypus_septemcinctus_MACN-Ma_13220_Cr.mrk.json
Error: Loading D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/.mrkps.json Templates/Dasypus_septemcinctus_MACN-Ma_13220_Cr.mrk.json - load failed.
I have exported landmarks coordinates in .pts file into .mrks.json format to use in ALPACA. I share these files with you so you can see if there is any inconsistency between them
(Attachment Chaetophractus_vellerosus_MACN-Ma_35.337_Cr.mrk.json is missing)
(Attachment Chaetophractus_vellerosus_MACN-Ma_35.337_Cr.pts is missing)
These are errors at other set of specimens:
GetArrayItemsStringProperty: markups property is not an array
Traceback (most recent call last):
File “C:/ProgramData/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py”, line 951, in onApplyLandmarkMulti
logic.runLandmarkMultiprocess(
File “C:/ProgramData/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py”, line 1561, in runLandmarkMultiprocess
array = self.pairwiseAlignment(
File “C:/ProgramData/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py”, line 1618, in pairwiseAlignment
sourceLandmarks, sourceLMNode = self.loadAndScaleFiducials(
File “C:/ProgramData/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py”, line 2866, in loadAndScaleFiducials
sourceLandmarkNode = slicer.util.loadMarkups(fiducial)
File “C:\ProgramData[slicer.org](http://slicer.org/)\Slicer 5.6.2\bin\Python\slicer\util.py”, line 863, in loadMarkups
return loadNodeFromFile(filename, “MarkupsFile”)
File “C:\ProgramData[slicer.org](http://slicer.org/)\Slicer 5.6.2\bin\Python\slicer\util.py”, line 734, in loadNodeFromFile
raise RuntimeError(errorMessage)
RuntimeError: Failed to load node from file: D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/.mrkps.json Templates/Dasypus_septemcinctus_MACN-Ma_13220_Cr.mrk.json
Error: Loading D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/.mrkps.json Templates/Dasypus_septemcinctus_MACN-Ma_13220_Cr.mrk.json - load failed.
I have exported landmarks coordinates in .pts file into .mrks.json format to use in ALPACA as templates. I share these files with you so you can see if there is any inconsistency between them. These coordinates correspond to the same specimen. The targets are made from photogrammetry
{
“@schema”: “https://raw.githubusercontent.com/Slicer/Slicer/main/Modules/Loadable/Markups/Resources/Schema/markups-schema-v1.0.0.json#”,
“markups”: {
“type”: “Fiducial”,
“coordinateSystem”: “LPS”,
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“position”: [37.7541, -52.0187, -18.2158]
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“position”: [30.2662, -47.3469, -21.1346]
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“position”: [31.9175, -49.9682, -20.7883]
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{
“label”: “S013”,
“position”: [31.797, -53.7763, -17.8025]
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{
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{
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“position”: [30.9929, -69.1461, -12.278]
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{
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“position”: [30.9918, -71.5094, -14.5013]
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{
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“position”: [34.3105, -70.4575, -14.0783]
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“position”: [31.4022, -38.953, -15.2223]
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“position”: [22.4619, -23.9445, -26.5049]
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“position”: [20.4977, -25.435, -24.278]
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“position”: [18.7416, -30.3332, -17.9179]
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“position”: [17.446, -38.1628, -17.5902]
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“position”: [19.4214, -33.9421, -14.2639]
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“position”: [21.8329, -33.0524, -11.2296]
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“position”: [23.1472, -33.3997, -9.3929]
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{
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“position”: [24.5036, -33.9116, -7.8147]
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“position”: [25.2918, -36.8534, -6.0291]
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“label”: “S044”,
“position”: [23.9786, -40.2156, -4.7997]
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“label”: “S045”,
“position”: [21.1875, -42.5474, -5.8932]
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“position”: [19.5283, -44.1903, -6.7014]
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“position”: [19.8511, -46.0734, -18.7032]
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“position”: [21.7544, -51.9731, -12.4034]
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“position”: [20.8697, -51.3901, -9.0766]
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{
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“position”: [18.9073, -57.9055, -11.5839]
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“position”: [18.7048, -54.2922, -7.3396]
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{
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“position”: [16.1963, -57.7051, -9.886]
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“position”: [34.6841, -14.2653, -25.2997]
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“position”: [37.0433, -36.4687, -23.1609]
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{
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“position”: [37.6952, -45.9551, -21.9758]
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“position”: [34.7364, -49.763, -23.5898]
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{
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“position”: [37.3222, -65.9218, -21.5574]
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{
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“position”: [33.2897, -71.4615, -16.0583]
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{
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{
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“position”: [16.0445, -67.8117, -30.3247]
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{
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“position”: [21.5849, -72.0162, -27.4299]
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{
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“position”: [31.5413, -12.0461, -31.3811]
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“position”: [34.0389, -2.4053, -30.5007]
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{
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“position”: [40.2004, -61.6671, -43.9936]
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{
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{
“label”: “S144”,
“position”: [17.2653, -67.5293, -33.0731]
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{
“label”: “S145”,
“position”: [38.2605, -71.2373, -26.9116]
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{
“label”: “S146”,
“position”: [36.9145, -67.4786, -42.3566]
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]
}
}
Version 1.0
146
S000 2.8203892e+001 -1.1775056e+001 -2.3414427e+001
S001 3.0778339e+001 -2.5995820e+000 -2.3561563e+001
S002 3.4536510e+001 -5.6057725e+000 -2.4469601e+001
S003 3.4364937e+001 -8.8592491e+000 -2.5044052e+001
S004 3.2550316e+001 -1.5468665e+001 -2.1276091e+001
S005 3.2648094e+001 -1.6161158e+001 -2.1028259e+001
S006 3.3074837e+001 -2.3193558e+001 -1.9532482e+001
S007 3.4829262e+001 -3.5287754e+001 -1.6771318e+001
S008 3.7628445e+001 -4.5621021e+001 -1.5477632e+001
S009 3.7754074e+001 -5.2018688e+001 -1.8215755e+001
S010 3.0266197e+001 -4.7346924e+001 -2.1134647e+001
S011 3.1917503e+001 -4.9968178e+001 -2.0788300e+001
S012 3.1797047e+001 -5.3776272e+001 -1.7802547e+001
S013 3.4078903e+001 -5.4511723e+001 -1.8870293e+001
S014 3.2730743e+001 -6.6573700e+001 -1.5997721e+001
S015 3.4470612e+001 -6.7438446e+001 -1.4077168e+001
S016 3.0992935e+001 -6.9146103e+001 -1.2277966e+001
S017 3.0991760e+001 -7.1509377e+001 -1.4501346e+001
S018 3.4310520e+001 -7.0457512e+001 -1.4078334e+001
S019 2.2060146e+001 -5.9818462e+001 -4.3684082e+000
S020 2.1218260e+001 -5.1530048e+001 -6.1669579e+000
S021 2.3733116e+001 -5.2936459e+001 -5.6438751e+000
S022 2.6359438e+001 -5.2396542e+001 -4.9870329e+000
S023 2.7259277e+001 -4.8711231e+001 -4.3993988e+000
S024 2.7203257e+001 -4.5158283e+001 -3.6921730e+000
S025 2.7583710e+001 -4.2851627e+001 -3.6906662e+000
S026 2.8618486e+001 -4.0803650e+001 -4.1693802e+000
S027 3.0353962e+001 -3.9373985e+001 -6.3381186e+000
S028 3.0133957e+001 -3.7810352e+001 -8.5109453e+000
S029 2.9356766e+001 -3.6718594e+001 -1.1053646e+001
S030 3.0265148e+001 -3.6717892e+001 -1.3274181e+001
S031 3.1402176e+001 -3.8952961e+001 -1.5222285e+001
S032 2.9789217e+001 -3.6895931e+001 -1.4402830e+001
S033 2.8739861e+001 -3.2914822e+001 -1.4861589e+001
S034 2.2461861e+001 -2.3944500e+001 -2.6504852e+001
S035 2.0497692e+001 -2.5435041e+001 -2.4277985e+001
S036 1.8741589e+001 -3.0333200e+001 -1.7917927e+001
S037 1.7446049e+001 -3.8162823e+001 -1.7590176e+001
S038 1.9421360e+001 -3.3942131e+001 -1.4263936e+001
S039 2.1832890e+001 -3.3052376e+001 -1.1229595e+001
S040 2.3147213e+001 -3.3399673e+001 -9.3928747e+000
S041 2.4503611e+001 -3.3911594e+001 -7.8146896e+000
S042 2.5291807e+001 -3.6853374e+001 -6.0290756e+000
S043 2.3978638e+001 -4.0215633e+001 -4.7996693e+000
S044 2.1187462e+001 -4.2547375e+001 -5.8932190e+000
S045 1.9528311e+001 -4.4190296e+001 -6.7014236e+000
S046 1.9851114e+001 -4.6073391e+001 -1.8703199e+001
S047 2.5261887e+001 -4.8042530e+001 -1.7980755e+001
S048 2.1754414e+001 -5.1973076e+001 -1.2403437e+001
S049 2.0869701e+001 -5.1390148e+001 -9.0766048e+000
S050 1.8907341e+001 -5.7905518e+001 -1.1583946e+001
S051 1.8704790e+001 -5.4292221e+001 -7.3396263e+000
S052 1.9585770e+001 -5.1711567e+001 -6.3110199e+000
S053 2.1187420e+001 -4.7515999e+001 -5.2966461e+000
S054 2.1471031e+001 -4.4852329e+001 -4.7529984e+000
S055 1.8790253e+001 -4.6660694e+001 -7.1210604e+000
S056 1.7753567e+001 -5.0515369e+001 -7.6184292e+000
S057 1.6819408e+001 -5.3886772e+001 -8.4897118e+000
S058 1.6196255e+001 -5.7705112e+001 -9.8859844e+000
S059 1.6437931e+001 -6.2461246e+001 -1.1054459e+001
S060 1.6392998e+001 -6.8000389e+001 -1.3244669e+001
S061 1.4816048e+001 -6.9535538e+001 -1.8758024e+001
S062 1.4452999e+001 -6.8852859e+001 -2.3915335e+001
S063 1.4894501e+001 -6.7180824e+001 -2.7827620e+001
S064 1.5992802e+001 -6.6075790e+001 -3.0577782e+001
S065 1.6375408e+001 -4.9616615e+001 -3.1436424e+001
S066 2.4360672e+001 -2.2429655e+001 -2.8804110e+001
S067 3.1806364e+001 -1.4697181e-001 -2.7604492e+001
S068 3.5324547e+001 -5.5974030e+000 -2.5632322e+001
S069 3.4684059e+001 -1.4265275e+001 -2.5299656e+001
S070 3.7043304e+001 -3.6468708e+001 -2.3160879e+001
S071 3.7695232e+001 -4.5955063e+001 -2.1975784e+001
S072 3.4736427e+001 -4.9763046e+001 -2.3589832e+001
S073 3.6835999e+001 -5.8694553e+001 -2.2567848e+001
S074 3.7322250e+001 -6.5921761e+001 -2.1557407e+001
S075 3.3289673e+001 -7.1461456e+001 -1.6058271e+001
S076 3.0309364e+001 -7.2452667e+001 -2.3995840e+001
S077 2.3021870e+001 -6.3884960e+001 -6.1466179e+000
S078 1.6044460e+001 -6.7811676e+001 -3.0324745e+001
S079 2.1584852e+001 -7.2016235e+001 -2.7429905e+001
S080 3.1541256e+001 -1.2046052e+001 -3.1381081e+001
S081 3.4038925e+001 -2.4053276e+000 -3.0500710e+001
S082 3.5926498e+001 -5.3750110e+000 -2.8289598e+001
S083 3.4926533e+001 -8.9477234e+000 -2.6252705e+001
S084 3.5997173e+001 -1.5530206e+001 -2.8763672e+001
S085 3.6298313e+001 -1.6434547e+001 -2.8702299e+001
S086 3.7129807e+001 -2.3462729e+001 -2.8729969e+001
S087 4.0027691e+001 -3.5999371e+001 -2.8236446e+001
S088 4.2395966e+001 -4.6241890e+001 -2.6449509e+001
S089 4.0461857e+001 -5.2514160e+001 -2.3789141e+001
S090 3.3261078e+001 -4.7452145e+001 -2.8202747e+001
S091 3.4731133e+001 -5.0233154e+001 -2.7125645e+001
S092 3.6887531e+001 -5.4403027e+001 -2.8465101e+001
S093 3.6785618e+001 -5.5652073e+001 -2.6332338e+001
S094 3.7775875e+001 -6.7136078e+001 -2.7769321e+001
S095 4.0837002e+001 -6.8700783e+001 -2.7339920e+001
S096 3.9525200e+001 -7.0608444e+001 -3.1188450e+001
S097 3.6209305e+001 -7.2157143e+001 -2.9414167e+001
S098 3.8909046e+001 -7.2095398e+001 -2.9129383e+001
S099 4.0200432e+001 -6.1667080e+001 -4.3993645e+001
S100 3.7398094e+001 -5.3321556e+001 -4.4702721e+001
S101 3.9510311e+001 -5.4466728e+001 -4.2917725e+001
S102 4.1815590e+001 -5.3588799e+001 -4.1316795e+001
S103 4.2833290e+001 -5.0520016e+001 -4.1518463e+001
S104 4.3688332e+001 -4.7485905e+001 -4.2066120e+001
S105 4.4094719e+001 -4.5389523e+001 -4.2160805e+001
S106 4.4879913e+001 -4.2315399e+001 -4.1191002e+001
S107 4.4491020e+001 -4.1217266e+001 -3.9759857e+001
S108 4.4266563e+001 -4.0444138e+001 -3.7902008e+001
S109 4.1474983e+001 -3.8452530e+001 -3.7090164e+001
S110 3.9257603e+001 -3.7951019e+001 -3.3574574e+001
S111 3.8929035e+001 -4.0390106e+001 -3.1155710e+001
S112 3.7548256e+001 -3.8221024e+001 -3.2828369e+001
S113 3.7646145e+001 -3.3641750e+001 -3.4329426e+001
S114 2.5176464e+001 -2.4529577e+001 -3.3209145e+001
S115 2.6438164e+001 -2.5667011e+001 -3.5980324e+001
S116 2.8878529e+001 -3.0946255e+001 -3.9691833e+001
S117 2.6552765e+001 -4.0283356e+001 -3.9510857e+001
S118 3.0173580e+001 -3.4481163e+001 -4.0881130e+001
S119 3.5197971e+001 -3.4791752e+001 -4.1954517e+001
S120 3.8083908e+001 -3.5473503e+001 -4.2193398e+001
S121 4.0603561e+001 -3.7406338e+001 -4.2447514e+001
S122 4.1884129e+001 -3.9465599e+001 -4.2984901e+001
S123 4.1497437e+001 -4.1850986e+001 -4.4112942e+001
S124 3.8798256e+001 -4.4199303e+001 -4.5207592e+001
S125 3.7017654e+001 -4.5813831e+001 -4.5914665e+001
S126 3.0246994e+001 -4.7206131e+001 -3.6153229e+001
S127 3.2778465e+001 -4.9301655e+001 -3.6235279e+001
S128 3.2881302e+001 -5.2151318e+001 -3.8256912e+001
S129 3.4576530e+001 -5.3998070e+001 -4.1319828e+001
S130 3.1747345e+001 -6.0650360e+001 -4.2454689e+001
S131 3.5125706e+001 -5.6334484e+001 -4.5201920e+001
S132 3.6731594e+001 -5.2859695e+001 -4.5682499e+001
S133 3.8012394e+001 -4.9451187e+001 -4.5585274e+001
S134 3.9224903e+001 -4.6692352e+001 -4.5618877e+001
S135 3.5289963e+001 -4.9802593e+001 -4.6156792e+001
S136 3.3856667e+001 -5.4238827e+001 -4.6178432e+001
S137 3.1679638e+001 -5.8109940e+001 -4.5557899e+001
S138 3.1952938e+001 -6.3407082e+001 -4.4679535e+001
S139 2.9874466e+001 -6.8487144e+001 -4.3163662e+001
S140 2.5781071e+001 -7.0617882e+001 -4.0004940e+001
S141 2.2319035e+001 -7.0230461e+001 -3.7911186e+001
S142 1.9592731e+001 -6.9020515e+001 -3.5746052e+001
S143 1.7265312e+001 -6.7529312e+001 -3.3073055e+001
S144 3.8260548e+001 -7.1237328e+001 -2.6911633e+001
S145 3.6914497e+001 -6.7478607e+001 -4.2356552e+001
I will need two models and the markup file to see where these are coming from.
Ok, I can´t send by this mail. I´ll sending by your mail.
You need to upload somewhere you can share the link to file (dropbox, onedrive, google drive etc…)