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Feb 13, 2021 at 17:56 history edited Vince CC BY-SA 4.0
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Feb 13, 2021 at 13:01 comment added Kazuhito Complicated. Apart from how QGIS has treated the CRS by the on-the-fly projection, there would be multiple issues related to the map itself. Geological Survey of Japan has used Bonne projection to map surface geology prior to 1952. Hence the LatLong GCPs you used to georeference were on ellipsoid Bessel 1841. On the other hand your DEM was on WGS84. On and around Japan, they usually show 400m+ displacement between them. EPSG 30162 was built on older Japanese mapping system (and used Bessel 1841). Current CRS for that area (Kyushu) would be EPSG: 3097 (on GRS80).
Feb 13, 2021 at 4:32 history asked Ben CC BY-SA 4.0