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Because this external software, for example smt-maestro,
was needed to resolve this problem.
The side effect was that the resulting centeroid file was correct read by openpnp and liteplacer importer.
Can you confirm that the first problem is resolved?
Result:
Ref,X,Y,rot,Footprint,PartNumber,Value,,,
R2,14.05,4.4,180,0603,RC0603FR-071ML,RES 1M OHM 1/10W 1%,,,,
R6,26.06,18.35,180,1206,ERJ-P08J180V,18 Ohm resistor 2/3w,,,,
R5,23.4,3.1,180,1206,RC1206JR-0715RL,15 Ohm resistor 1/4w,,,,
R7,23.8,26.8,180,1206,RC1206JR-0730RL,30 Ohm resistor 1/4w,,,,
F1,3.25,25.9,180,1812,0ZCC0150BF2C,PTC RESTTBLE 1.50A 24V CHIP 1812,,,,
X1,14.02,7.79,0,3-SMD,PBRC16.00MR50X000,16mhz ceramic osc,,,,
U1,13.85,14.3,0,44 QFN-EP,IC MCU 8BIT 16KB FLASH 44QFN,ATMEGA16U4-MU,,,,
U2,15,15.3,180,6-SMD,High Power LEDs - Multi-Color RGB,XZCB25MO24DG25X111S,,,,
C3,1.85,22.9,0,CAP_0603,,1uF,,,,
C4,5.95,28.8,0,CAP_0603,,1uF,,,,
C5,8.6,27.75,90,CAP_0603,,.1uF,,,,
C2,7.2,12.25,270,CAP_0603,GRM188R61A105KA61D,1uF,,,,
C1,13.25,19,180,CAP_0603,GRM188R71E104KA01D,.1uF,,,,
Q1,27.86,4.27,270,MOSFETN,,BUK9277-55A,,,,
Q2,26.29,15.21,0,MOSFETN,,BUK9277-55A,,,,
Q3,27.44,25.63,90,MOSFETN,,BUK9277-55A,,,,
R10,27.75,22.8,180,RES_0603,,10k,,,,
R4,7.15,14.7,180,RES_0603,,22,,,,
R8,27.75,7.3,0,RES_0603,,10k,,,,
R9,23.66,15.1,90,RES_0603,,10k,,,,
R3,7.15,16,180,RES_0603,MCT06030C2209FP500,22,,,,
R1,9.05,1.9,0,RES_0603,RC0603JR-0710KL,10k,,,,
J2,2.11,14.92,270,uUSB SMT,10118192-0001LF,CONN USB MICRO B RECPT SMT R/A,,,,