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6cc19306
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Jim Regetz
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# Full sequence of (bash) commands used to transform the original
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# organisms@jupiter home directory structure to the new layers@atlas
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# home directory structure. This was done after first rsyncing the
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# entire ~organisms home directory from jupiter onto atlas at
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# /home/organisms, and creating a new 'layers' user with home directory
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# /home/layers.
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#
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# Jim Regetz
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# NCEAS
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# Created on 23-Feb-2012
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export ORGANISMS="/home/organisms"
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export LAYERS="/home/layers"
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86eb951b
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Jim Regetz
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export REPO="."
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6cc19306
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Jim Regetz
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#=======================================================================
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# set up some directories
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#=======================================================================
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# create master home for all datasets
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mkdir $LAYERS/data
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mkdir $LAYERS/data/climate
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mkdir $LAYERS/data/terrain
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mkdir $LAYERS/data/land-cover
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# create (temporary) home for associated readmes, documentation, etc
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mkdir $LAYERS/documentation
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mkdir $LAYERS/documentation/climate
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mkdir $LAYERS/documentation/terrain
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mkdir $LAYERS/documentation/land-cover
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# create (temporary) home for processing code
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mkdir $LAYERS/code
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mkdir $LAYERS/code/climate
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mkdir $LAYERS/code/terrain
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mkdir $LAYERS/code/land-cover
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# create (temporary?) home for everything else
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f3cc83bd
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Jim Regetz
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mkdir $LAYERS/commons
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mkdir $LAYERS/commons/terrain
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mkdir $LAYERS/commons/land-cover
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mkdir $LAYERS/commons/cruft
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6cc19306
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Jim Regetz
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#=======================================================================
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# carry out file migration, reorganization, and cleanup
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#=======================================================================
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#========#
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# Marine #
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#========#
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# easy one ... just delete, as we're retaining this work on the original
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# server
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rm -rf Marine/
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#=====#
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# DEM #
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#=====#
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#
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# SRTM 1km
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#
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# migrate original rar file
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mkdir $LAYERS/data/terrain/dem-cgiar-srtm-1km-ascii
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mv $ORGANISMS/DEM/SRTM_1km_ASCII.rar $LAYERS/data/terrain/dem-cgiar-srtm-1km-ascii/srtm_1km_ascii.rar
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# migrate clipped/reprojected bil
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mv $ORGANISMS/Oregon_SRTM $LAYERS/data/terrain/dem-cgiar-srtm-1km-OR/
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#
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# CGIAR SRTM 90m
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#
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# SRTM 90m zips
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mv $ORGANISMS/DEM/cgiarSrtm/archive $LAYERS/data/terrain/dem-cgiar-srtm-90m-zips
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# SRTM 90m tiles and processed descendents
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# first flatten out SRTM 90m directories
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mv $ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1/Tiles_Resampled/Mosaiced \
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$ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1_Resampled_Mosaiced
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mv $ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1/Tiles_Resampled \
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$ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1_Resampled
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# now migrate to ~layers
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mv $ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1 \
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$LAYERS/data/terrain/dem-cgiar-srtm-90m-asc
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mv $ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1_Resampled \
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$LAYERS/data/terrain/dem-cgiar-srtm-90m-asc-resamp
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mv $ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1_Resampled_Mosaiced \
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$LAYERS/data/terrain/dem-cgiar-srtm-90m-asc-resamp-mosaic
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# SRTM 90m tile index (zipped)
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mkdir $LAYERS/data/terrain/dem-cgiar-srtm-90m-index-zip
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mv $ORGANISMS/DEM/cgiarSrtm/srtm-tile-index_v4.1_shp.zip \
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$LAYERS/data/terrain/dem-cgiar-srtm-90m-index-zip/
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# SRTM 90m tile index (unzipped)
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mv $ORGANISMS/DEM/cgiarSrtm/index \
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$LAYERS/data/terrain/dem-cgiar-srtm-90m-index
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# move readme to deal with later
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mv $ORGANISMS/DEM/cgiarSrtm/README.txt $LAYERS/documentation/terrain/cgiar-srtm-90m-readme.txt
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# remove now-empty directory
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rmdir $ORGANISMS/DEM/cgiarSrtm
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ff302b98
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Jim Regetz
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#
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# ASTER GDEM1
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#
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# --- first do cleanup ---
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# remove duplicate files (confirmed by diffing)
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rm $ORGANISMS/DEM/asterGdem/ListOfEurasiaDropouts.txt
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rm $ORGANISMS/DEM/asterGdem/BadFileCheckLogVulcanAfterNewFiles.txt
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rm $ORGANISMS/DEM/asterGdem/BadFileCheckLogBeforeCorrection.txt
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# remove misc trivial/obsolete scripts
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rm $ORGANISMS/DEM/asterGdem/translateToImg.sh
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rm $ORGANISMS/DEM/asterGdem/incorrectTilesJuly2011/replacedJuly4/copyDownTifs.sh
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rm $ORGANISMS/DEM/asterGdem/incorrectTilesJuly2011/checkBadAsterGDEMFiles.sh
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# remove file listings and/or gdalinfo output with insufficient context
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rm $ORGANISMS/DEM/asterGdem/incorrectTilesJuly2011/BadFileCheckLogVulcanAfterNewFiles.txt
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rm $ORGANISMS/DEM/asterGdem/incorrectTilesJuly2011/ListOfEurasiaDropouts.txt
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rm $ORGANISMS/DEM/asterGdem/incorrectTilesJuly2011/BadFileCheckLogBeforeCorrection.txt
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rm $ORGANISMS/DEM/asterGdem/incorrectTilesJuly2011/replacedJuly4/Juy4NumFiles.txt
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rm $ORGANISMS/DEM/asterGdem/incorrectTilesJuly2011/replacedJuly4/July4NumFiles.txt
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rm $ORGANISMS/DEM/asterGdem/incorrectTilesJuly2011/replacedJuly4/July4Files.txt
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# remove now-empty directory
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rmdir $ORGANISMS/DEM/asterGdem/incorrectTilesJuly2011/replacedJuly4
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# remove reeves-generated ArcGIS aux/rrd files
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find $ORGANISMS/DEM/asterGdem/ -name "*.aux" -exec rm {} \;
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find $ORGANISMS/DEM/asterGdem/ -name "*.rrd" -exec rm {} \;
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# remove gdal-generated metadata files
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find $ORGANISMS/DEM/asterGdem/ -name "*.tif.aux.xml" -exec rm {} \;
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find $ORGANISMS/DEM/asterGdem/ -name "*.dem.aux.xml" -exec rm {} \;
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# remove img tiles (for which we have the original tifs in all cases)
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rm $ORGANISMS/DEM/asterGdem/TilesBelowN59/*.{img,img.aux.xml}
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# migrate Robinson R scripts
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mv -i $ORGANISMS/DEM/asterGdem/R_files \
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$LAYERS/code/terrain/asterGdem
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# migrate Robinson GDEM1 assessment docs (incl QGIS project files)
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f3cc83bd
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Jim Regetz
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mkdir $LAYERS/commons/terrain/gdem-v1
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ff302b98
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Jim Regetz
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mv -i $ORGANISMS/DEM/asterGdem/*.ods \
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f3cc83bd
|
Jim Regetz
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$LAYERS/commons/terrain/gdem-v1/
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ff302b98
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Jim Regetz
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find $ORGANISMS/DEM/asterGdem -name "*.qgs" -exec mv {} \
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f3cc83bd
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Jim Regetz
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$LAYERS/commons/terrain/gdem-v1/ \;
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ff302b98
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Jim Regetz
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# migrate remaining tree as the GDEM v1 dataset itself
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mv $ORGANISMS/DEM/asterGdem \
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$LAYERS/data/terrain/dem-aster-gdem1-30m-orig
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6cc19306
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Jim Regetz
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#
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# ASTER GDEM2
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#
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# remove gdal-generated metadata files
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77ed568c
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Jim Regetz
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rm $ORGANISMS/DEM/asterGdem2/*.tif.aux.xml
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rm $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset/*.tif.aux.xml
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rm $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset/Mosaiced/N59to60/*.tif.aux.xml
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6cc19306
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Jim Regetz
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# first flatten out directories
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mv $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset/Mosaiced/N59to60 \
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$ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset-Mosaiced-N59to60
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mv $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset/Mosaiced \
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$ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset-Mosaiced
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mv $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset \
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$ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset
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# now migrate to ~layers
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mv $ORGANISMS/DEM/asterGdem2 \
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$LAYERS/data/terrain/dem-aster-gdem2-30m-orig
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mv $ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset \
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$LAYERS/data/terrain/dem-aster-gdem2-90m-resamp
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mv $ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset-Mosaiced \
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$LAYERS/data/terrain/dem-aster-gdem2-90m-resamp-mosaic-N60to83
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mv $ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset-Mosaiced-N59to60 \
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$LAYERS/data/terrain/dem-aster-gdem2-90m-resamp-mosaic-N59to60
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#
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# CDED
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#
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# remove duplicate files (confirmed by diffing)
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rm $ORGANISMS/DEM/CanadaDED/084b\ \(1\).zip
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rm $ORGANISMS/DEM/CanadaDED/Monday/114p\ \(1\).zip
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rm $ORGANISMS/DEM/CanadaDED/mosaicMostCanadaDem.sh
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rm $ORGANISMS/DEM/CanadaDED/Monday/mergeCanada104105.{tif,aux,rrd}
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# migrate zips
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mkdir $LAYERS/data/terrain/dem-cded-zip
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mv -i $ORGANISMS/DEM/CanadaDED/0*.zip \
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$LAYERS/data/terrain/dem-cded-zip/
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/1*.zip \
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$LAYERS/data/terrain/dem-cded-zip/
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# migrate documentation
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mv -i $ORGANISMS/DEM/CanadaDED/CanadaDEDTechRefManual.pdf \
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$LAYERS/documentation/terrain/cded-TechRefManual.pdf
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# migrate some stuff to experimental, for now...
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f3cc83bd
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Jim Regetz
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mkdir $LAYERS/commons/terrain/dem-cded
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6cc19306
|
Jim Regetz
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# ... vrt files, what the heck
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mv -i $ORGANISMS/DEM/CanadaDED/*demFile.vrt \
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f3cc83bd
|
Jim Regetz
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$LAYERS/commons/terrain/dem-cded/
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6cc19306
|
Jim Regetz
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# ... misc scripts and log files
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mv -i $ORGANISMS/DEM/CanadaDED/in*DemFile.txt \
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f3cc83bd
|
Jim Regetz
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$LAYERS/commons/terrain/dem-cded/
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6cc19306
|
Jim Regetz
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mv -i $ORGANISMS/DEM/CanadaDED/unzipFiles.sh \
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| 201 |
f3cc83bd
|
Jim Regetz
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$LAYERS/commons/terrain/dem-cded/unzipFiles_0.sh
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| 202 |
6cc19306
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Jim Regetz
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/unzipFiles.sh \
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| 203 |
f3cc83bd
|
Jim Regetz
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$LAYERS/commons/terrain/dem-cded/unzipFiles_1.sh
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| 204 |
6cc19306
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Jim Regetz
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mv -i $ORGANISMS/DEM/CanadaDED/{.,/Monday}/*.sh \
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| 205 |
f3cc83bd
|
Jim Regetz
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$LAYERS/commons/terrain/dem-cded/
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| 206 |
6cc19306
|
Jim Regetz
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mv -i $ORGANISMS/DEM/CanadaDED/*.log \
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| 207 |
f3cc83bd
|
Jim Regetz
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$LAYERS/commons/terrain/dem-cded/
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| 208 |
6cc19306
|
Jim Regetz
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mv -i $ORGANISMS/DEM/CanadaDED/moscomps \
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| 209 |
f3cc83bd
|
Jim Regetz
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$LAYERS/commons/terrain/dem-cded/
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| 210 |
6cc19306
|
Jim Regetz
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/filesToMosaic \
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| 211 |
f3cc83bd
|
Jim Regetz
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$LAYERS/commons/terrain/dem-cded/
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| 212 |
6cc19306
|
Jim Regetz
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/*Log \
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| 213 |
f3cc83bd
|
Jim Regetz
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$LAYERS/commons/terrain/dem-cded/
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| 214 |
6cc19306
|
Jim Regetz
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# remove extracted data (no plans to use it), after determining that these are
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# the set of files matching globs "*.dem" or "*_fgdc_*.{xml,html}"
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# # ---- bash code ---#
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# # list out all files contained in the zips
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| 218 |
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# cd $LAYERS/data/terrain/dem-cded-zip && ls \
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| 219 |
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# | xargs -I+ sh -c 'unzip -l + | grep -e " 200[7-9]-"' \
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| 220 |
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# | awk '{print $4}' > /home/layers/cded-extracts.txt
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| 221 |
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# # ----- R code -----#
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| 222 |
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# # read in the extracted file names
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| 223 |
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# extracts <- scan("/home/layers/cded-extracts.txt", what="")
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| 224 |
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# # read in all CDED files stored in the organisms home dir
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| 225 |
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# files <- list.files(path=c("/home/organisms/DEM/CanadaDED",
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# "/home/organisms/DEM/CanadaDED/Monday"))
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# # note that all zip contents had been extracted (...based on filename)
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| 228 |
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# all(extracts %in% files)
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| 229 |
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# ## [1] TRUE
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| 230 |
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# # isolate files *not* extracted from the zips
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| 231 |
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# others <- setdiff(files, extracts)
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| 232 |
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# # show that all extracted filenames match one of two patterns
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| 233 |
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# all(grepl("dem$", extracts) | grepl("_fgdc_", extracts))
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| 234 |
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# ## [1] TRUE
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| 235 |
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# # and show that no other files match these
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| 236 |
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# any(grepl("dem$", others) | grepl("_fgdc_", others))
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# ## [1] FALSE
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| 238 |
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# # ------------------#
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| 239 |
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rm $ORGANISMS/DEM/CanadaDED/*.dem
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| 240 |
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rm $ORGANISMS/DEM/CanadaDED/*_fgdc_*.{xml,html}
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| 241 |
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rm $ORGANISMS/DEM/CanadaDED/Monday/*.dem
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| 242 |
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rm $ORGANISMS/DEM/CanadaDED/Monday/*_fgdc_*.{xml,html}
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| 243 |
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# now remove items of uncertain origin
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| 244 |
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rm $ORGANISMS/DEM/CanadaDED/*.dem.aux.xml
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| 245 |
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rm $ORGANISMS/DEM/CanadaDED/Monday/*.dem.aux.xml
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| 246 |
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rm $ORGANISMS/DEM/CanadaDED/*dem?.{aux,rrd}
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| 247 |
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rm $ORGANISMS/DEM/CanadaDED/Monday/*dem?.{aux,rrd}
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| 248 |
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rm $ORGANISMS/DEM/CanadaDED/*demFile.{aux,rrd,vrt.aux,tif.aux.xml,tif,vrt.rrd}
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| 249 |
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rm $ORGANISMS/DEM/CanadaDED/CDEMPlySRTMDf.aux
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| 250 |
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rm -r $ORGANISMS/DEM/CanadaDED/cdemplysrtmdf
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| 251 |
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rm -r $ORGANISMS/DEM/CanadaDED/info
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| 252 |
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# what the hell, remove other generated tifs because I really can't account for
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| 253 |
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# the details of their creation...
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| 254 |
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rm $ORGANISMS/DEM/CanadaDED/CanadaDemMos*.{tif,rrd,aux,aux.xml,tif.xml,img,vat.dbf}
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| 255 |
|
|
rm $ORGANISMS/DEM/CanadaDED/mergeCanada104105.{tif,aux,rrd}
|
| 256 |
|
|
|
| 257 |
|
|
# remove now-empty directories
|
| 258 |
|
|
rmdir $ORGANISMS/DEM/CanadaDED/Monday
|
| 259 |
|
|
rmdir $ORGANISMS/DEM/CanadaDED
|
| 260 |
|
|
|
| 261 |
|
|
|
| 262 |
|
|
#
|
| 263 |
|
|
# FUSED DEM
|
| 264 |
|
|
#
|
| 265 |
|
|
|
| 266 |
|
|
# remove gdal-generated metadata files
|
| 267 |
77ed568c
|
Jim Regetz
|
rm $ORGANISMS/DEM/GlobalProduct/*.tif.aux.xml
|
| 268 |
6cc19306
|
Jim Regetz
|
# migrate to ~layers
|
| 269 |
|
|
mv $ORGANISMS/DEM/GlobalProduct $LAYERS/data/terrain/dem-fused
|
| 270 |
|
|
|
| 271 |
|
|
#
|
| 272 |
|
|
# GTOPO30
|
| 273 |
|
|
#
|
| 274 |
|
|
|
| 275 |
ff302b98
|
Jim Regetz
|
# migrate Nunokawa-clipped data -- first version
|
| 276 |
|
|
mkdir $LAYERS/data/terrain/dem-usgs-gtopo30-clipped-nunokawa-v1
|
| 277 |
|
|
find $ORGANISMS/DEM/usgsGTOPO30 -name "*_Clipped.dem" \
|
| 278 |
|
|
-exec mv {} $LAYERS/data/terrain/dem-usgs-gtopo30-clipped-nunokawa-v1 \;
|
| 279 |
|
|
# migrate Nunokawa-clipped data -- second version
|
| 280 |
|
|
mv -i $ORGANISMS/DEM/Yuni/Data/GTOPO30 \
|
| 281 |
|
|
$LAYERS/data/terrain/dem-usgs-gtopo30-clipped-nunokawa-v2
|
| 282 |
|
|
|
| 283 |
|
|
# migrate Robinson-clipped data
|
| 284 |
|
|
mkdir $LAYERS/data/terrain/dem-usgs-gtopo30-clipped-robinson
|
| 285 |
|
|
mv $ORGANISMS/DEM/asterGdem/N59to81_E20to59/e020n90/E020N90_clipped.dem \
|
| 286 |
|
|
$LAYERS/data/terrain/dem-usgs-gtopo30-clipped-robinson/
|
| 287 |
|
|
mv $ORGANISMS/DEM/asterGdem/N59to81_E140to179/e140n90/E140N90_clipped.dem \
|
| 288 |
|
|
$LAYERS/data/terrain/dem-usgs-gtopo30-clipped-robinson/
|
| 289 |
|
|
mv $ORGANISMS/DEM/asterGdem/N59to81_W140to101/w140n90/W140N90_clipped.dem \
|
| 290 |
|
|
$LAYERS/data/terrain/dem-usgs-gtopo30-clipped-robinson/
|
| 291 |
|
|
mv $ORGANISMS/DEM/asterGdem/N59to81_E60to99/USGS_ErosDEM_N59to81E60to99/E060N90_clipped.dem \
|
| 292 |
|
|
$LAYERS/data/terrain/dem-usgs-gtopo30-clipped-robinson/
|
| 293 |
|
|
mv $ORGANISMS/DEM/asterGdem/N59to81_W60to21/w060n90/W060N90_clipped.dem \
|
| 294 |
|
|
$LAYERS/data/terrain/dem-usgs-gtopo30-clipped-robinson/
|
| 295 |
|
|
mv $ORGANISMS/DEM/asterGdem/N59to81_W100to61/w100n90/W100N90_clipped.dem \
|
| 296 |
|
|
$LAYERS/data/terrain/dem-usgs-gtopo30-clipped-robinson/
|
| 297 |
|
|
mv $ORGANISMS/DEM/asterGdem/N59to81_E100to139/e100n90/E100N90_clipped.dem \
|
| 298 |
|
|
$LAYERS/data/terrain/dem-usgs-gtopo30-clipped-robinson/
|
| 299 |
|
|
mv $ORGANISMS/DEM/asterGdem/N59to81_W180to141/w180n90/W180N90_clipped.dem \
|
| 300 |
|
|
$LAYERS/data/terrain/dem-usgs-gtopo30-clipped-robinson/
|
| 301 |
|
|
mv $ORGANISMS/DEM/asterGdem/N59to81_W20toE19/w020n90/W020N90_clipped.dem \
|
| 302 |
|
|
$LAYERS/data/terrain/dem-usgs-gtopo30-clipped-robinson/
|
| 303 |
|
|
# remove mysterious extra GeoTIFF (sans extension) with timestamp similar to
|
| 304 |
|
|
# the above, but that was mysteriously the same as the like-named
|
| 305 |
|
|
# clipped-nunokawa-v1 file (created months later)
|
| 306 |
|
|
rm $ORGANISMS/DEM/asterGdem/N59to81_E60to99/USGS_ErosDEM_N59to81E60to99/E060N90_Clipped
|
| 307 |
|
|
|
| 308 |
6cc19306
|
Jim Regetz
|
# remove gdal-generated metadata file
|
| 309 |
77ed568c
|
Jim Regetz
|
rm $ORGANISMS/DEM/usgsGTOPO30/e020n90/*.DEM.aux.xml
|
| 310 |
ff302b98
|
Jim Regetz
|
# remove Mac OS X file metadata cruft
|
| 311 |
|
|
find $ORGANISMS/DEM/usgsGTOPO30 -name ".DS_Store" -exec rm {} \;
|
| 312 |
|
|
find $ORGANISMS/DEM/usgsGTOPO30 -name "._*" -exec rm {} \;
|
| 313 |
|
|
# now migrate original (?) GTOPO30 data
|
| 314 |
6cc19306
|
Jim Regetz
|
mv $ORGANISMS/DEM/usgsGTOPO30 $LAYERS/data/terrain/dem-usgs-gtopo30
|
| 315 |
ff302b98
|
Jim Regetz
|
# confirmed that we had identical copies of the above GTOPO DEM data
|
| 316 |
|
|
# # ---- bash code ---#
|
| 317 |
|
|
# for i in `find $ORGANISMS/DEM/asterGdem -name "*.DEM" -exec basename {} \;`
|
| 318 |
|
|
# do
|
| 319 |
|
|
# diff -q `find $ORGANISMS/DEM/asterGdem -name $i` \
|
| 320 |
|
|
# `find $LAYERS/data/terrain/dem-usgs-gtopo30 -name $i`
|
| 321 |
|
|
# done
|
| 322 |
|
|
# # ------------------#
|
| 323 |
|
|
# (and in fact manually confirmed that the containing directories themselves
|
| 324 |
|
|
# were duplicated, albeit with different names)
|
| 325 |
|
|
# ...so remove the duplicates...
|
| 326 |
|
|
find $ORGANISMS/DEM/asterGdem -name "*.DEM" | sed 's/\/[EW].*//' | xargs -I+ rm -r +
|
| 327 |
6cc19306
|
Jim Regetz
|
|
| 328 |
|
|
#
|
| 329 |
|
|
# GMTED2010
|
| 330 |
|
|
#
|
| 331 |
|
|
|
| 332 |
|
|
# remove gdal-generated metadata files
|
| 333 |
77ed568c
|
Jim Regetz
|
rm $ORGANISMS/GMTED2010/*.tif.aux.xml
|
| 334 |
6cc19306
|
Jim Regetz
|
# remove ArcMap(?) schema lock file
|
| 335 |
|
|
rm $ORGANISMS/GMTED2010/GMTED2010_Spatial_Metadata/GMTED2010_Spatial_Metadata.shp.IGSKMNCNWK00726.6284.8844.sr.lock
|
| 336 |
|
|
# migrate original (I think) downloaded data (OR only)
|
| 337 |
|
|
mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-tiles
|
| 338 |
|
|
mv $ORGANISMS/GMTED2010/30N150W_20101117_gmted_mea300.tif \
|
| 339 |
|
|
$LAYERS/data/terrain/dem-gmted2010-mea300-OR-tiles/
|
| 340 |
|
|
mv $ORGANISMS/GMTED2010/30N120W_20101117_gmted_mea300.tif \
|
| 341 |
|
|
$LAYERS/data/terrain/dem-gmted2010-mea300-OR-tiles/
|
| 342 |
|
|
# migrate merged OR tiles (i think)
|
| 343 |
|
|
mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-mosaic
|
| 344 |
|
|
mv $ORGANISMS/GMTED2010/OR_Coverage.tif \
|
| 345 |
|
|
$LAYERS/data/terrain/dem-gmted2010-mea300-OR-mosaic/
|
| 346 |
|
|
# migrate OR clipped/reprojected data
|
| 347 |
|
|
mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-tif
|
| 348 |
|
|
mv $ORGANISMS/GMTED2010/OR_ClippedToMODIS_InSinu.tif \
|
| 349 |
|
|
$LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-tif/
|
| 350 |
|
|
mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-bil
|
| 351 |
|
|
mv $ORGANISMS/GMTED2010/OR_ClippedToMODIS_InSinu.{prj,hdr,bil} \
|
| 352 |
|
|
$LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-bil/
|
| 353 |
|
|
# migrate shapefile
|
| 354 |
|
|
mv $ORGANISMS/GMTED2010/GMTED2010_Spatial_Metadata \
|
| 355 |
|
|
$LAYERS/data/terrain/dem-gmted2010-spatial-metadata
|
| 356 |
|
|
# migrate documentation
|
| 357 |
|
|
mv $ORGANISMS/GMTED2010/of2011-1073.pdf $LAYERS/documentation/terrain/gmted2010-report.pdf
|
| 358 |
|
|
mv $ORGANISMS/GMTED2010/ReadMe $LAYERS/documentation/terrain/gmted2010-readme.txt
|
| 359 |
|
|
# remove now-empty directory
|
| 360 |
|
|
rmdir $ORGANISMS/GMTED2010
|
| 361 |
|
|
|
| 362 |
|
|
#
|
| 363 |
|
|
# Nunokawa content
|
| 364 |
|
|
#
|
| 365 |
|
|
|
| 366 |
77ed568c
|
Jim Regetz
|
# regetz notes about nunokawa boundary datasets
|
| 367 |
|
|
# aster2/aster2_*_82N.tif # Int16 59N-82N GDEM2 elevation
|
| 368 |
|
|
# aster2/aster2_*_below.tif # Int16 59N-60N GDEM2 elevation
|
| 369 |
|
|
# aster2/aster2_*_above.tif # Int16 60N-61N GDEM2 elevation
|
| 370 |
|
|
# aster2/aster2_*_straddle.tif # Int16 59N-61N GDEM2 elevation (GDEM2 above, GDEM2 below)
|
| 371 |
|
|
# aster2/aster2_*_straddle_a.tif # Flt32 59N-61N GDEM2-based aspect
|
| 372 |
|
|
# aster2/aster2_*_straddle_s.tif # Flt32 59N-61N GDEM2-based slope
|
| 373 |
|
|
# aster2/aster2_*_below_blendgau.tif # Flt32 59N-60N GDEM2/SRTM blended elevation
|
| 374 |
|
|
# aster2/fused_*_straddle.tif # Int16 59N-61N GDEM2/SRTM unblended elevation (GDEM2 above, SRTM below)
|
| 375 |
|
|
# aster2/fused_*_straddle_a.tif # Flt32 59N-61N unblended-based aspect
|
| 376 |
|
|
# aster2/fused_*_straddle_s.tif # Flt32 59N-61N unblended-based aspect
|
| 377 |
|
|
# aster2/fused_*_blendgau.tif # Int16 59N-61N GDEM2/SRTM blended elevation (GDEM2 above, blended below)
|
| 378 |
|
|
# aster2/fused_*_blendgau_a.tif # Flt32 59N-61N blend-based aspect
|
| 379 |
|
|
# aster2/fused_*_blendgau_s.tif # Flt32 59N-61N blend-based aspect
|
| 380 |
|
|
# srtm/srtm_*_below.tif # Int16 59N-60N SRTM elevation
|
| 381 |
|
|
# srtm/srtm_*_below_a.tif # Flt32 59N-60N SRTM-based aspect
|
| 382 |
|
|
# srtm/srtm_*_below_below_s.tif # Flt32 59N-60N SRTM-based slope
|
| 383 |
|
|
# aster2/aster.vrt # VRT - GDEM2 from ~59N-82N (with 1/2-pixel offset)
|
| 384 |
|
|
# srtm/srtm.vrt # VRT - SRTM from ~55N-60N (with 1/2-pixel offset)
|
| 385 |
6cc19306
|
Jim Regetz
|
|
| 386 |
|
|
# remove duplicate file
|
| 387 |
|
|
rm $ORGANISMS/DEM/Yuni/Data/aster2/fused_w180w141
|
| 388 |
|
|
# remove redundant backup files (but leaving some others)
|
| 389 |
|
|
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/aspect.r~
|
| 390 |
|
|
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/check.r~
|
| 391 |
|
|
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/meanElv.r~
|
| 392 |
|
|
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/meanElv_onlyN59.r~
|
| 393 |
|
|
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/
|
| 394 |
|
|
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/assembling.r~
|
| 395 |
|
|
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/gaussian.r~
|
| 396 |
|
|
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/mkVrt_Tiff.r~
|
| 397 |
|
|
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/slope_aspect.r~
|
| 398 |
77ed568c
|
Jim Regetz
|
|
| 399 |
|
|
# migrate scripts
|
| 400 |
6cc19306
|
Jim Regetz
|
mv $ORGANISMS/DEM/Yuni/scripts \
|
| 401 |
|
|
$LAYERS/code/terrain/nunokawa-scripts
|
| 402 |
|
|
# migrate documents
|
| 403 |
|
|
mv -i $ORGANISMS/DEM/Yuni/documents \
|
| 404 |
|
|
$LAYERS/documentation/terrain/nunokawa-documents
|
| 405 |
|
|
mv -i $ORGANISMS/DEM/Yuni/missing_gdem2_tiles.txt \
|
| 406 |
|
|
$LAYERS/documentation/terrain/nunokawa-documents/
|
| 407 |
|
|
mv -i $ORGANISMS/DEM/Yuni/metadata.txt \
|
| 408 |
|
|
$LAYERS/documentation/terrain/nunokawa-documents/
|
| 409 |
77ed568c
|
Jim Regetz
|
# migrate remaining Data contents to 60N boundary dir
|
| 410 |
|
|
mv -i $ORGANISMS/DEM/Yuni/Data \
|
| 411 |
f3cc83bd
|
Jim Regetz
|
$LAYERS/commons/terrain/north-60
|
| 412 |
77ed568c
|
Jim Regetz
|
|
| 413 |
|
|
# remove now-empty directories
|
| 414 |
|
|
rmdir $ORGANISMS/DEM/Yuni
|
| 415 |
|
|
rmdir $ORGANISMS/DEM
|
| 416 |
6cc19306
|
Jim Regetz
|
|
| 417 |
|
|
#
|
| 418 |
|
|
# Remaining DEM content
|
| 419 |
|
|
#
|
| 420 |
|
|
|
| 421 |
|
|
mv $ORGANISMS/DEM/DEM_ProcessingScripts $LAYERS/code/terrain/
|
| 422 |
|
|
mv $ORGANISMS/DEM/ReadMeInProgress.txt $LAYERS/documentation/terrain/misc-partial-readme.txt
|
| 423 |
|
|
|
| 424 |
|
|
|
| 425 |
|
|
rm $ORGANISMS/DEM/checklog
|
| 426 |
f3cc83bd
|
Jim Regetz
|
mv $ORGANISMS/DEM/checkBadAsterGDEMFiles.sh $LAYERS/commons/cruft/
|
| 427 |
|
|
mv $ORGANISMS/DEM/CheckGDEMLog.txt $LAYERS/commons/cruft/
|
| 428 |
6cc19306
|
Jim Regetz
|
|
| 429 |
|
|
|
| 430 |
|
|
#=========#
|
| 431 |
|
|
# CLIMATE #
|
| 432 |
|
|
#=========#
|
| 433 |
|
|
|
| 434 |
|
|
#
|
| 435 |
|
|
# CRU
|
| 436 |
|
|
#
|
| 437 |
|
|
|
| 438 |
|
|
# migrate original gz data from CRU (or so it appears...)
|
| 439 |
|
|
mkdir $LAYERS/data/climate/cru-ts-3.0-1901-2006-gzip
|
| 440 |
|
|
mv $ORGANISMS/CRU_TS_3.0/*.gz $LAYERS/data/climate/cru-ts-3.0-1901-2006-gzip/
|
| 441 |
|
|
# I confirmed that the gunzipped files are identical to the gz contents (by
|
| 442 |
|
|
# gunzipping to /tmp and then diffing):w
|
| 443 |
|
|
# ...so let's delete the uncompressed versions
|
| 444 |
|
|
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.pre.nc
|
| 445 |
|
|
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.tmn.nc
|
| 446 |
|
|
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.tmp.nc
|
| 447 |
|
|
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.tmx.nc
|
| 448 |
|
|
# migrate extracted ASCII grid files
|
| 449 |
|
|
mv $ORGANISMS/CRU_TS_3.0/PRE $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-pre
|
| 450 |
|
|
mv $ORGANISMS/CRU_TS_3.0/TMN $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-tmn
|
| 451 |
|
|
mv $ORGANISMS/CRU_TS_3.0/TMP $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-tmp
|
| 452 |
|
|
mv $ORGANISMS/CRU_TS_3.0/TMX $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-tmx
|
| 453 |
|
|
# migrate R script for asc extraction
|
| 454 |
|
|
mv -i $ORGANISMS/CRU_TS_3.0/R/cru_3.0_data_extract.r $LAYERS/code/climate/
|
| 455 |
|
|
# rename then migrate readmes
|
| 456 |
|
|
rename 's/(Read_Me)/clim-cru-ts-3.0-\1/' $ORGANISMS/CRU_TS_3.0/Read_Me_*.txt
|
| 457 |
|
|
mv $ORGANISMS/CRU_TS_3.0/*Read_Me_*.txt $LAYERS/documentation/climate/
|
| 458 |
|
|
# now remove empty directory structure
|
| 459 |
|
|
find $ORGANISMS/CRU_TS_3.0 -depth -type d -exec rmdir {} \;
|
| 460 |
|
|
|
| 461 |
|
|
#
|
| 462 |
|
|
# GSOD
|
| 463 |
|
|
#
|
| 464 |
|
|
|
| 465 |
|
|
# for now, just move the whole thing as-is
|
| 466 |
|
|
mv $ORGANISMS/gsod $LAYERS/data/climate/gsod
|
| 467 |
|
|
|
| 468 |
|
|
#
|
| 469 |
|
|
# GHCN
|
| 470 |
|
|
#
|
| 471 |
|
|
|
| 472 |
|
|
# for now, just move the whole thing as-is
|
| 473 |
|
|
mv $ORGANISMS/ghcn $LAYERS/data/climate/ghcn
|
| 474 |
|
|
|
| 475 |
|
|
#
|
| 476 |
|
|
# MODIS LST
|
| 477 |
|
|
#
|
| 478 |
|
|
|
| 479 |
|
|
# migrate MOD11A1 V4 daily 1km L3 LST (March 1-7, 2000)
|
| 480 |
|
|
mv $ORGANISMS/MODIS\ LST/MOD11A1.004 $LAYERS/data/climate/MOD11A1.004-daily-1km-L3-LST/
|
| 481 |
|
|
# migrate MOD11A2 V4 8-day 1km L3 LST (March 5, 2000)
|
| 482 |
|
|
mkdir $LAYERS/data/climate/MOD11A2.004-8day-1km-L3-LST
|
| 483 |
|
|
mv $ORGANISMS/MODIS\ LST/2000.03.05 $LAYERS/data/climate/MOD11A2.004-8day-1km-L3-LST/
|
| 484 |
|
|
# also remove identical copies of the MOD11A2 data (confirmed by diffing)
|
| 485 |
|
|
rm $ORGANISMS/Modis_2000.03.05/MOD11A2.A2000065.*.hdf
|
| 486 |
|
|
rm $ORGANISMS/Modis_2000.03.05/MOD11A2.A2000065.*.hdf.xml
|
| 487 |
|
|
rmdir $ORGANISMS/Modis_2000.03.05
|
| 488 |
|
|
# remove now-empty directory
|
| 489 |
|
|
rmdir $ORGANISMS/MODIS\ LST
|
| 490 |
|
|
|
| 491 |
|
|
#
|
| 492 |
|
|
# MODIS LST -- Oregon
|
| 493 |
|
|
#
|
| 494 |
|
|
|
| 495 |
|
|
# migrate original MODIS OR hdfs (2001-2010?)
|
| 496 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-orig
|
| 497 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/MOD11A1.*.hdf \
|
| 498 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-orig/
|
| 499 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/MOD11A1.*.hdf.xml \
|
| 500 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-orig/
|
| 501 |
|
|
# migrate original MODIS OR hdfs (2000, not used)
|
| 502 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-orig-2000
|
| 503 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/2000\ _WithheldFromAVG/MOD11A1.A2000*.hdf \
|
| 504 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-orig-2000/
|
| 505 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/2000\ _WithheldFromAVG/MOD11A1.A2000*.hdf.xml \
|
| 506 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-orig-2000/
|
| 507 |
|
|
# migrate ClearDayCov OR img extracts (2001-2010?)
|
| 508 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img
|
| 509 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/MOD11A1.*.img \
|
| 510 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img/
|
| 511 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/MOD11A1.*.img.aux.xml \
|
| 512 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img/
|
| 513 |
|
|
# migrate ClearDayCov OR img extracts (2000, not used)
|
| 514 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-2000
|
| 515 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/2000_WithheldFromAVG/MOD11A1.A2000*.005_ClearDay.img \
|
| 516 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-2000/
|
| 517 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/2000_WithheldFromAVG/MOD11A1.A2000*.005_ClearDay.img.aux.xml \
|
| 518 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-2000/
|
| 519 |
|
|
|
| 520 |
|
|
# migrate renamed ClearDayCov OR img extracts (2001-2010?)
|
| 521 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed
|
| 522 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/*.img \
|
| 523 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed/
|
| 524 |
|
|
# migrate renamed ClearDayCov OR img extracts (2000, not used)
|
| 525 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-2000
|
| 526 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/2000_WithheldFromAVG/MOD11A1.A.2000.*.img \
|
| 527 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-2000/
|
| 528 |
|
|
|
| 529 |
|
|
# migrate renamed ClearDayCov OR img extracts with corrected pixels
|
| 530 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-fixed
|
| 531 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/*.img \
|
| 532 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-fixed/
|
| 533 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/*.img.aux.xml \
|
| 534 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-fixed/
|
| 535 |
|
|
|
| 536 |
|
|
# migrate ClearDayCov OR daily avg tiles
|
| 537 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img
|
| 538 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day*.img \
|
| 539 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img/
|
| 540 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day*.img.aux.xml \
|
| 541 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img/
|
| 542 |
|
|
# migrate ClearDayCov OR daily avg mosaic imgs
|
| 543 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img
|
| 544 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.img \
|
| 545 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img
|
| 546 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.img.aux.xml \
|
| 547 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img
|
| 548 |
|
|
# migrate ClearDayCov OR daily avg mosaic bils
|
| 549 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil
|
| 550 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.prj \
|
| 551 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/
|
| 552 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.bil \
|
| 553 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/
|
| 554 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.bil.aux.xml \
|
| 555 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/
|
| 556 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.hdr \
|
| 557 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/
|
| 558 |
|
|
|
| 559 |
|
|
# migrate ClearDayCov OR monthly avg tiles
|
| 560 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-tiles-img
|
| 561 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/*_AVG_Scaled.img \
|
| 562 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-tiles-img/
|
| 563 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/*_AVG_Scaled.img.aux.xml \
|
| 564 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-tiles-img/
|
| 565 |
|
|
# migrate ClearDayCov OR monthly avg mosaic imgs
|
| 566 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-img
|
| 567 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.img \
|
| 568 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-img/
|
| 569 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.img.aux.xml \
|
| 570 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-img/
|
| 571 |
|
|
# migrate ClearDayCov OR monthly avg mosaic bils
|
| 572 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil
|
| 573 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.prj \
|
| 574 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/
|
| 575 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.bil \
|
| 576 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/
|
| 577 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.bil.aux.xml \
|
| 578 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/
|
| 579 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.hdr \
|
| 580 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/
|
| 581 |
|
|
|
| 582 |
|
|
# migrate *old* (wrong?) ClearDayCov OR daily avg tiles
|
| 583 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD
|
| 584 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Tiles_Old/Day_*_Average_Scaled_*.img \
|
| 585 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD/
|
| 586 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Tiles_Old/Day_*_Average_Scaled_*.img.aux.xml \
|
| 587 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD/
|
| 588 |
|
|
# migrate *old* (wrong?) ClearDayCov OR daily avg mosaics
|
| 589 |
|
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img-OLD
|
| 590 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Mosaic_Old/Day_*_ClearDay_Average.img \
|
| 591 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img-OLD/
|
| 592 |
|
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Mosaic_Old/Day_*_ClearDay_Average.img.aux.xml \
|
| 593 |
|
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img-OLD/
|
| 594 |
|
|
|
| 595 |
|
|
# remove identical copies of (old) ClearDayCov daily avgs for tile h08v04
|
| 596 |
|
|
# *Note*: I first confirmed that these are duplicate copies:
|
| 597 |
|
|
# for i in {1..366};
|
| 598 |
|
|
# do
|
| 599 |
|
|
# diff -q $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old/Day_"$i"_Average_Scaled.img \
|
| 600 |
|
|
# $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD/Day_"$i"_Average_Scaled_h08v04.img
|
| 601 |
|
|
# done
|
| 602 |
|
|
rm $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old/Day_{1..366}_Average_Scaled.img
|
| 603 |
|
|
rm $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old/Day_{1..366}_Average_Scaled.img.aux.xml
|
| 604 |
|
|
# remove now-empty directory
|
| 605 |
|
|
rmdir $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old
|
| 606 |
|
|
|
| 607 |
|
|
# remove misc bil statistics (stx) files)
|
| 608 |
|
|
rm $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day11_Mosaic_DailyAvg_Scaled.stx
|
| 609 |
|
|
rm $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day1_Mosaic_DailyAvg_Scaled.stx
|
| 610 |
|
|
rm $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/AprMosaic_MonthlyAvg_Scaled.stx
|
| 611 |
|
|
|
| 612 |
|
|
# remove pyc file
|
| 613 |
|
|
rm $ORGANISMS/MODIS_LST_Oregon/GDAL_Extract_ClearDay_from_HDF_Files.pyc
|
| 614 |
|
|
|
| 615 |
|
|
# move and (if needed) rename documentation files
|
| 616 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/1\ ReadMe\ First.txt \
|
| 617 |
|
|
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-orig-readme.txt
|
| 618 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/MODIS_Oregon_ProcessingInfo.doc \
|
| 619 |
|
|
$LAYERS/documentation/climate/
|
| 620 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/2000\ _WithheldFromAVG/ReadMe \
|
| 621 |
|
|
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-orig-2000-readme.txt
|
| 622 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/1\ ReadMe\ First.txt \
|
| 623 |
|
|
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-clearday-readme.txt
|
| 624 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/1\ ReadMe\ First \
|
| 625 |
|
|
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-clearday-img-renamed-fixed-readme.txt
|
| 626 |
|
|
|
| 627 |
|
|
# move scripts
|
| 628 |
|
|
mkdir $LAYERS/code/climate/modis-lst-oregon
|
| 629 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/GDAL_Extract_ClearDay_from_HDF_Files.py \
|
| 630 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 631 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/QCTagCheck \
|
| 632 |
|
|
$LAYERS/code/climate/modis-lst-oregon/QCTagCheck.py
|
| 633 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ConvertMODIStobil.py \
|
| 634 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 635 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/DayAVGCalcs_h08v04TIles.r \
|
| 636 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 637 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/DayAVGCalcs_h09v04TIles.r \
|
| 638 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 639 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/LST_Mosaicing_DailyAvgs.r \
|
| 640 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 641 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/LST_Mosaicing_MonthlyAvgs.R \
|
| 642 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 643 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/Conversion_hdf_to_img.py \
|
| 644 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 645 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/h09v04Tiles_BadPixelCorrection.r \
|
| 646 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 647 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/h08v04Tiles_BadPixelCorrection.r \
|
| 648 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 649 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/Convert\ MODIS\ Day\ of\ Year\ to\ Date\ File\ Name.py \
|
| 650 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 651 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/MonthlyAvgCalcs_h08v04Tiles.r \
|
| 652 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 653 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/MonthlyAvgCalcs_h09v04Tiles.r \
|
| 654 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 655 |
|
|
|
| 656 |
|
|
# move last few things...
|
| 657 |
|
|
mv -i $ORGANISMS/MODIS_LST_Oregon/hdf.txt \
|
| 658 |
f3cc83bd
|
Jim Regetz
|
$LAYERS/commons/cruft/clim-MOD11A1.004-OR-orig-hdf.txt
|
| 659 |
6cc19306
|
Jim Regetz
|
mv -i $ORGANISMS/MODIS_LST_Oregon/SDS_PctFills.txt \
|
| 660 |
f3cc83bd
|
Jim Regetz
|
$LAYERS/commons/cruft/clim-MOD11A1.004-OR-orig-SDS_PctFills.txt
|
| 661 |
6cc19306
|
Jim Regetz
|
|
| 662 |
|
|
# remove all the now-empty directories...
|
| 663 |
|
|
# tree $ORGANISMS/MODIS_LST_Oregon
|
| 664 |
|
|
# /home/organisms/MODIS_LST_Oregon
|
| 665 |
|
|
# .
|
| 666 |
|
|
# ├── 2000 _WithheldFromAVG
|
| 667 |
|
|
# └── ClearDayGDAL
|
| 668 |
|
|
# ├── ClearDay_DailyAverage_Mosaic_Old
|
| 669 |
|
|
# ├── ClearDay_DailyAverage_Tiles_Old
|
| 670 |
|
|
# ├── ClearDay_Original_IMG_Extracts
|
| 671 |
|
|
# │  ├── 2000_WithheldFromAVG
|
| 672 |
|
|
# │  └── ByDate
|
| 673 |
|
|
# │  ├── 2000_WithheldFromAVG
|
| 674 |
|
|
# │  └── BadPixelsCorrected_Tiles
|
| 675 |
|
|
# ├── NewClearDay_DailyAvgs_Mosaics
|
| 676 |
|
|
# ├── NewClearDay_DailyAvgs_Tiles
|
| 677 |
|
|
# ├── NewClearDay_MonthlyAvgs_Mosaics
|
| 678 |
|
|
# └── NewClearDay_MonthlyAvgs_Tiles
|
| 679 |
|
|
find $ORGANISMS/MODIS_LST_Oregon -depth -type d -exec rmdir {} \;
|
| 680 |
|
|
|
| 681 |
|
|
# last but not least, deal with top level R directory
|
| 682 |
|
|
# ...move some (old? superceded?) scripts
|
| 683 |
|
|
mv -i $ORGANISMS/R/ReClass Clear Day Rasters h08v04.r \
|
| 684 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 685 |
|
|
mv -i $ORGANISMS/R/Calc Clear Day Daily Avg.r \
|
| 686 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 687 |
|
|
mv -i $ORGANISMS/R/Mosaic Clear Day Average Grids.r \
|
| 688 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 689 |
|
|
mv -i $ORGANISMS/R/Calc Clear Day Monthly Avg.r \
|
| 690 |
|
|
$LAYERS/code/climate/modis-lst-oregon/
|
| 691 |
|
|
# don't know how this was created, but it's clearly derived data...
|
| 692 |
|
|
mv -i $ORGANISMS/R/Modis_LSTdaily_climatology $LAYERS/data/clim-modis-lstdaily
|
| 693 |
|
|
# remove now-empty directory
|
| 694 |
|
|
rmdir $ORGANISMS/R
|
| 695 |
|
|
|
| 696 |
|
|
#
|
| 697 |
|
|
# TRMM
|
| 698 |
|
|
#
|
| 699 |
|
|
|
| 700 |
|
|
# this was an *empty* directory! removing...
|
| 701 |
|
|
rmdir $ORGANISMS/TRMM
|
| 702 |
|
|
|
| 703 |
|
|
#
|
| 704 |
|
|
# WorldClim
|
| 705 |
|
|
#
|
| 706 |
|
|
|
| 707 |
|
|
# migrate each one into its own directory
|
| 708 |
|
|
mkdir $LAYERS/data/climate/worldclim-bio-30s-esri-zip
|
| 709 |
|
|
mv $ORGANISMS/WorldClim/bio_30s_esri.zip $LAYERS/data/climate/worldclim-bio-30s-esri-zip/
|
| 710 |
|
|
mkdir $LAYERS/data/climate/worldclim-prec-30s-esri-zip
|
| 711 |
|
|
mv $ORGANISMS/WorldClim/prec_30s_esri.zip $LAYERS/data/climate/worldclim-prec-30s-esri-zip/
|
| 712 |
|
|
mkdir $LAYERS/data/climate/worldclim-tmax-30s-esri-zip
|
| 713 |
|
|
mv $ORGANISMS/WorldClim/tmax_30s_esri.zip $LAYERS/data/climate/worldclim-tmax-30s-esri-zip/
|
| 714 |
|
|
mkdir $LAYERS/data/climate/worldclim-tmean-30s-esri-zip
|
| 715 |
|
|
mv $ORGANISMS/WorldClim/tmean_30s_esri.zip $LAYERS/data/climate/worldclim-tmean-30s-esri-zip/
|
| 716 |
|
|
mkdir $LAYERS/data/climate/worldclim-tmin-30s-esri-zip
|
| 717 |
|
|
mv $ORGANISMS/WorldClim/tmin_30s_esri.zip $LAYERS/data/climate/worldclim-tmin-30s-esri-zip/
|
| 718 |
|
|
# remove now-empty directory
|
| 719 |
|
|
rmdir $ORGANISMS/WorldClim
|
| 720 |
|
|
|
| 721 |
|
|
|
| 722 |
|
|
#============#
|
| 723 |
|
|
# LAND COVER #
|
| 724 |
|
|
#============#
|
| 725 |
|
|
|
| 726 |
|
|
#
|
| 727 |
|
|
# GLCNMO
|
| 728 |
|
|
#
|
| 729 |
|
|
|
| 730 |
|
|
# for now, just move the whole thing as-is
|
| 731 |
f3cc83bd
|
Jim Regetz
|
mv $ORGANISMS/GLCNMO $LAYERS/commons/land-cover/
|
| 732 |
6cc19306
|
Jim Regetz
|
|
| 733 |
0fe2dd49
|
Jim Regetz
|
# now remove some cruft
|
| 734 |
|
|
rm $LAYERS/commons/land-cover/GLCNMO/lc11/lc11/Thumbs.db
|
| 735 |
|
|
# migrate AML scripts into repository
|
| 736 |
|
|
mkdir $REPO/land-cover/research/GLCNMO
|
| 737 |
|
|
mv -i $LAYERS/commons/land-cover/GLCNMO/merge_lc1.aml \
|
| 738 |
|
|
$REPO/land-cover/research/GLCNMO/
|
| 739 |
|
|
mv -i $LAYERS/commons/land-cover/GLCNMO/merge_lc.aml \
|
| 740 |
|
|
$REPO/land-cover/research/GLCNMO/
|
| 741 |
|
|
mv -i $LAYERS/commons/land-cover/GLCNMO/tiffgrid.aml \
|
| 742 |
|
|
$REPO/land-cover/research/GLCNMO/
|
| 743 |
|
|
|
| 744 |
6cc19306
|
Jim Regetz
|
#
|
| 745 |
|
|
# GlobCover
|
| 746 |
|
|
#
|
| 747 |
|
|
# migrate what seems like the original data (?)
|
| 748 |
|
|
mkdir $LAYERS/data/land-cover/GlobCover-v2.2
|
| 749 |
|
|
mv -i $ORGANISMS/GlobCoverv2.2/GLOBCOVER_200412_200606_V2.2_Global_CLA* \
|
| 750 |
|
|
$LAYERS/data/land-cover/GlobCover-v2.2/
|
| 751 |
|
|
# migrate mysterious derivatives of the above
|
| 752 |
|
|
mkdir $LAYERS/data/land-cover/GlobCover-v2.2-arcgis
|
| 753 |
|
|
mv -i $ORGANISMS/GlobCoverv2.2/globcov22_beh $LAYERS/data/land-cover/GlobCover-v2.2-arcgis/
|
| 754 |
|
|
mv -i $ORGANISMS/GlobCoverv2.2/globcoverv22 $LAYERS/data/land-cover/GlobCover-v2.2-arcgis/
|
| 755 |
|
|
# migrate reference info to documentation area
|
| 756 |
|
|
mv -i $ORGANISMS/GlobCoverv2.2/Globcover_* $LAYERS/documentation/land-cover/
|
| 757 |
|
|
# remove now-empty directory
|
| 758 |
|
|
rmdir $ORGANISMS/GlobCoverv2.2
|
| 759 |
|
|
|
| 760 |
|
|
#
|
| 761 |
|
|
# LandCover (whatever that is)
|
| 762 |
|
|
#
|
| 763 |
|
|
|
| 764 |
|
|
# remove gdal-generated metadata file
|
| 765 |
|
|
rm $ORGANISMS/LandCover/Layer10_Clip1.tif.aux.xml
|
| 766 |
|
|
# migrate original OR landcover tiles
|
| 767 |
|
|
mkdir $LAYERS/data/land-cover/lc-OR-tiles
|
| 768 |
|
|
mv $ORGANISMS/LandCover/Layer*_Clip[1-3].tif \
|
| 769 |
|
|
$LAYERS/data/land-cover/lc-OR-tiles/
|
| 770 |
|
|
# migrate OR landcover mosaics
|
| 771 |
|
|
mkdir $LAYERS/data/land-cover/lc-OR-mosaic
|
| 772 |
|
|
mv $ORGANISMS/LandCover/Layer*_Mosaic.tif \
|
| 773 |
|
|
$LAYERS/data/land-cover/lc-OR-mosaic/
|
| 774 |
|
|
# migrate OR clipped/reprojected landcover mosaics
|
| 775 |
|
|
mkdir $LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu
|
| 776 |
|
|
mv $ORGANISMS/LandCover/Layer*_ClippedToMODIS_Sinu.* \
|
| 777 |
|
|
$LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu/
|
| 778 |
|
|
# migrate OR multiband clipped/reprojected landcover mosaic
|
| 779 |
|
|
mkdir $LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu-multiband
|
| 780 |
|
|
mv $ORGANISMS/LandCover/Final_Multiband_SinuGrid.* \
|
| 781 |
|
|
$LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu-multiband/
|
| 782 |
|
|
# migrate documentation
|
| 783 |
|
|
mv $ORGANISMS/LandCover/ReadMe $LAYERS/documentation/land-cover/landcover-ReadMe.txt
|
| 784 |
|
|
mv $ORGANISMS/LandCover/LCT\ calculations.xlsx $LAYERS/documentation/land-cover/
|
| 785 |
|
|
mv $ORGANISMS/LandCover/landcover_method_v3.docx $LAYERS/documentation/land-cover/
|
| 786 |
|
|
# migrate scripts
|
| 787 |
|
|
mv $ORGANISMS/LandCover/CheckForNoDataValues_LandCoverFiles.txt $LAYERS/code/land-cover/
|
| 788 |
|
|
# remove now-empty directory
|
| 789 |
|
|
rmdir $ORGANISMS/LandCover
|
| 790 |
|
|
|
| 791 |
|
|
#
|
| 792 |
|
|
# Tree height
|
| 793 |
|
|
#
|
| 794 |
|
|
|
| 795 |
|
|
# migrate $ORGANISMS/Tree_height/Lefsky2010
|
| 796 |
|
|
mkdir $LAYERS/data/land-cover/treeheight-lefsky2010
|
| 797 |
|
|
mv $ORGANISMS/Tree_height/Lefsky2010/x2_080809_global.img \
|
| 798 |
|
|
$LAYERS/data/land-cover/treeheight-lefsky2010/
|
| 799 |
|
|
mv $ORGANISMS/Tree_height/Lefsky2010/p_080809_global.img* \
|
| 800 |
|
|
$LAYERS/data/land-cover/treeheight-lefsky2010/
|
| 801 |
|
|
# migrate associated publication do documentation area
|
| 802 |
|
|
mv $ORGANISMS/Tree_height/Lefsky2010/Lefsky\ et\ al.\ 2010\ GeoRLett.pdf \
|
| 803 |
|
|
$LAYERS/documentation/land-cover/treeheight-Lefsky2010-GeoRLett.pdf
|
| 804 |
|
|
# remove now-empty directory
|
| 805 |
|
|
rmdir $ORGANISMS/Tree_height/Lefsky2010
|
| 806 |
|
|
|
| 807 |
|
|
# migrate $ORGANISMS/Tree_height/Simard2011
|
| 808 |
|
|
mkdir $LAYERS/data/land-cover/treeheight-simard2011
|
| 809 |
|
|
mv $ORGANISMS/Tree_height/Simard2011/Simard_Pinto_3DGlobalVeg_JGR.tif \
|
| 810 |
|
|
$LAYERS/data/land-cover/treeheight-simard2011/
|
| 811 |
|
|
# remove gdal-generated metadata file
|
| 812 |
|
|
rm $ORGANISMS/Tree_height/Simard2011/Simard_Pinto_3DGlobalVeg_JGR.tif.aux.xml
|
| 813 |
|
|
# migrate clipped/reprojected file (bil)
|
| 814 |
|
|
mkdir $LAYERS/data/land-cover/treeheight-simard2011-OR-clip-proj-sinu-bil
|
| 815 |
|
|
mv $ORGANISMS/Tree_height/Simard2011/GlobalCanopy_ClippedToMODIS_InSinu.* \
|
| 816 |
|
|
$LAYERS/data/land-cover/treeheight-simard2011-OR-clip-proj-sinu-bil/
|
| 817 |
|
|
# migrate documentation
|
| 818 |
|
|
mv $ORGANISMS/Tree_height/Simard2011/SimardEtAl2011_GlobalTreeHeight_WithLIDAR.pdf \
|
| 819 |
|
|
$LAYERS/documentation/land-cover/treeheight-SimardEtAl_GlobalTreeHeight_WithLIDAR.pdf
|
| 820 |
|
|
mv $ORGANISMS/Tree_height/Simard2011/ReadMe \
|
| 821 |
|
|
$LAYERS/documentation/land-cover/treeheight-ReadMe.txt
|
| 822 |
|
|
# remove remaining files as per instructions from Natalie Robinson
|
| 823 |
|
|
rm $ORGANISMS/Tree_height/Simard2011/Test_Clip.tif
|
| 824 |
|
|
rm $ORGANISMS/Tree_height/Simard2011/GDALTranslate_test.*
|
| 825 |
|
|
rm $ORGANISMS/Tree_height/Simard2011/GDALTranslate_DT_int16.*
|
| 826 |
|
|
# remove now-empty directory
|
| 827 |
|
|
rmdir $ORGANISMS/Tree_height/Simard2011
|
| 828 |
|
|
|
| 829 |
|
|
# lastely, remove now-empty Tree_height directory
|
| 830 |
|
|
rmdir $ORGANISMS/Tree_height
|
| 831 |
|
|
|
| 832 |
|
|
|
| 833 |
|
|
#=================#
|
| 834 |
|
|
# Remaining stuff #
|
| 835 |
|
|
#=================#
|
| 836 |
|
|
|
| 837 |
|
|
#
|
| 838 |
|
|
# top level directory
|
| 839 |
|
|
#
|
| 840 |
|
|
|
| 841 |
|
|
# move top level notes
|
| 842 |
|
|
mv $ORGANISMS/Oregon_CaseStudy_FileProcessingInfo $LAYERS/documentation/
|
| 843 |
|
|
mv $ORGANISMS/ReProjection_To_MODIS $LAYERS/documentation/
|
| 844 |
|
|
mv $ORGANISMS/README.txt $LAYERS/documentation/organisms-homedir-readme.txt
|
| 845 |
|
|
mv $ORGANISMS/CHANGES.txt $LAYERS/documentation/organisms-homedir-changes.txt
|
| 846 |
|
|
# move old file extension summary
|
| 847 |
f3cc83bd
|
Jim Regetz
|
mv -i $ORGANISMS/file-extension-summary.txt $LAYERS/commons/cruft/
|
| 848 |
6cc19306
|
Jim Regetz
|
|
| 849 |
|
|
#
|
| 850 |
|
|
# Desktop
|
| 851 |
|
|
#
|
| 852 |
|
|
|
| 853 |
|
|
# move MRT installer to cruft
|
| 854 |
f3cc83bd
|
Jim Regetz
|
mv $ORGANISMS/Desktop/MRT_download_Linux $LAYERS/commons/cruft/
|
| 855 |
6cc19306
|
Jim Regetz
|
# remove orphaned bil metadata file
|
| 856 |
|
|
rm $ORGANISMS/Desktop/ASTER_Test.bil.aux.xml
|
| 857 |
|
|
# remove empty Desktop dir
|
| 858 |
|
|
rmdir $ORGANISMS/Desktop
|
| 859 |
|
|
|
| 860 |
|
|
#
|
| 861 |
|
|
# pyhdf
|
| 862 |
|
|
#
|
| 863 |
|
|
|
| 864 |
|
|
# move pyhdf package to cruft
|
| 865 |
f3cc83bd
|
Jim Regetz
|
mv $ORGANISMS/pyhdf $LAYERS/commons/cruft/
|
| 866 |
6cc19306
|
Jim Regetz
|
|
| 867 |
|
|
#
|
| 868 |
|
|
# GIS/GDD
|
| 869 |
|
|
#
|
| 870 |
|
|
|
| 871 |
|
|
# confirmed that /tmean contains unzipped tmean, except there are additional
|
| 872 |
|
|
# aux files presumably autogenerated by Arc -- I'm find with deleting them
|
| 873 |
|
|
# # ---- bash code ---#
|
| 874 |
|
|
# cd /tmp && unzip $ORGANISMS/GIS/GDD/tmean_30s_esri.zip
|
| 875 |
|
|
# diff -qr /tmp/tmean /home/organisms/GIS/GDD/tmean_30s_esri/tmean/
|
| 876 |
|
|
# done
|
| 877 |
|
|
# # ------------------#
|
| 878 |
|
|
# delete the uncompressed tmean_30s_esri directory
|
| 879 |
|
|
rm -r $ORGANISMS/GIS/GDD/tmean_30s_esri
|
| 880 |
|
|
|
| 881 |
|
|
# confirmed that WorldClim zips are identical to what we already have elsewhere
|
| 882 |
|
|
# # ---- bash code ---#
|
| 883 |
|
|
# for var in {'prec','tmin','tmax','tmean','bio'}
|
| 884 |
|
|
# do
|
| 885 |
|
|
# diff -s $ORGANISMS/GIS/GDD/"$var"_30s_esri.zip \
|
| 886 |
|
|
# $LAYERS/data/climate/worldclim-"$var"-30s-esri-zip/*.zip
|
| 887 |
|
|
# done
|
| 888 |
|
|
# done
|
| 889 |
|
|
# # ------------------#
|
| 890 |
|
|
# delete the duplicate worldclim zips
|
| 891 |
|
|
rm $ORGANISMS/GIS/GDD/prec_30s_esri.zip
|
| 892 |
|
|
rm $ORGANISMS/GIS/GDD/tmin_30s_esri.zip
|
| 893 |
|
|
rm $ORGANISMS/GIS/GDD/tmax_30s_esri.zip
|
| 894 |
|
|
rm $ORGANISMS/GIS/GDD/tmean_30s_esri.zip
|
| 895 |
|
|
rm $ORGANISMS/GIS/GDD/bio_30s_esri.zip
|
| 896 |
|
|
|
| 897 |
|
|
# confirmed that all MODIS files here are identical to (though in fact they are
|
| 898 |
|
|
# only a subset of) what we already have elsewhere
|
| 899 |
|
|
# # ---- bash code ---#
|
| 900 |
|
|
# for dir in `ls $ORGANISMS/GIS/GDD/MOD11A1.004`
|
| 901 |
|
|
# do
|
| 902 |
|
|
# echo checking "$dir"...
|
| 903 |
|
|
# ls $ORGANISMS/GIS/GDD/MOD11A1.004/"$dir" \
|
| 904 |
|
|
# | xargs -I+ \
|
| 905 |
|
|
# diff -q $ORGANISMS/GIS/GDD/MOD11A1.004/"$dir"/+ \
|
| 906 |
|
|
# $LAYERS/data/climate/MOD11A1.004-daily-1km-L3-LST/"$dir"/+
|
| 907 |
|
|
# done
|
| 908 |
|
|
# # ------------------#
|
| 909 |
|
|
# delete the duplicate MODIS data
|
| 910 |
|
|
# note that the last 3 dirs were already empty...
|
| 911 |
|
|
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.01/MOD11A1.A2000*.{hdf,hdf.xml}
|
| 912 |
|
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.01
|
| 913 |
|
|
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.02/MOD11A1.A2000*.{hdf,hdf.xml}
|
| 914 |
|
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.02
|
| 915 |
|
|
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.03/MOD11A1.A2000*.{hdf,hdf.xml}
|
| 916 |
|
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.03
|
| 917 |
|
|
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.04/MOD11A1.A2000*.{hdf,hdf.xml}
|
| 918 |
|
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.04
|
| 919 |
|
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.05
|
| 920 |
|
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.06
|
| 921 |
|
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.07
|
| 922 |
|
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004
|
| 923 |
|
|
|
| 924 |
|
|
# migrate remaining text (script?) file
|
| 925 |
|
|
mv $ORGANISMS/GIS/GDD/map\ algebra.txt $LAYERS/code/climate/gdd-worldclim-tmean-map-algebra.txt
|
| 926 |
|
|
# remove empty directory
|
| 927 |
|
|
rmdir $ORGANISMS/GIS/GDD
|
| 928 |
|
|
|
| 929 |
|
|
#
|
| 930 |
|
|
# GIS/terrain
|
| 931 |
|
|
#
|
| 932 |
|
|
|
| 933 |
|
|
# remove empty test directory
|
| 934 |
|
|
rmdir $ORGANISMS/GIS/terrain/test
|
| 935 |
|
|
# for now just migrate everything else to experimental area
|
| 936 |
f3cc83bd
|
Jim Regetz
|
mv $ORGANISMS/GIS/terrain $LAYERS/commons/terrain/arcgis
|
| 937 |
6cc19306
|
Jim Regetz
|
|
| 938 |
|
|
# remove empty directory
|
| 939 |
|
|
rmdir $ORGANISMS/GIS
|
| 940 |
|
|
|
| 941 |
|
|
#
|
| 942 |
|
|
# Oregon
|
| 943 |
|
|
#
|
| 944 |
|
|
|
| 945 |
77ed568c
|
Jim Regetz
|
# for now just migrate to experimental area
|
| 946 |
f3cc83bd
|
Jim Regetz
|
mv $ORGANISMS/Oregon $LAYERS/commons/oregon
|
| 947 |
6cc19306
|
Jim Regetz
|
|
| 948 |
|
|
#
|
| 949 |
|
|
# steph
|
| 950 |
|
|
#
|
| 951 |
|
|
|
| 952 |
|
|
# delete as per verbal instructions from Stephanie Pau
|
| 953 |
|
|
rm -rf $ORGANISMS/steph
|
| 954 |
|
|
|
| 955 |
|
|
#
|
| 956 |
|
|
# topo
|
| 957 |
|
|
#
|
| 958 |
|
|
|
| 959 |
86eb951b
|
Jim Regetz
|
# first migrate the whole thing to new commons area
|
| 960 |
|
|
mv $ORGANISMS/topo $LAYERS/commons/
|
| 961 |
|
|
# consolidate first set of dirs
|
| 962 |
|
|
mkdir $LAYERS/commons/topo/v1
|
| 963 |
|
|
mv -i $LAYERS/commons/topo/{experimental,scripts,tiles} \
|
| 964 |
|
|
$LAYERS/commons/topo/v1/
|
| 965 |
|
|
# consolidate second set of dirs
|
| 966 |
|
|
mv -i $LAYERS/commons/topo/experimental_2/topo \
|
| 967 |
|
|
$LAYERS/commons/topo/v2
|
| 968 |
|
|
rmdir $LAYERS/commons/topo/experimental_2
|
| 969 |
|
|
|
| 970 |
|
|
# remove ArcToolbox temporary files
|
| 971 |
|
|
rm $LAYERS/commons/topo/v2/topo/xx00003024.s
|
| 972 |
|
|
rm $LAYERS/commons/topo/v2/experimental/xx00013916.x
|
| 973 |
|
|
rm $LAYERS/commons/topo/v2/experimental/xx00003916.s
|
| 974 |
|
|
rm $LAYERS/commons/topo/v2/experimental/xx00013916.s
|
| 975 |
|
|
|
| 976 |
|
|
# consolidate first set of scripts into git repo
|
| 977 |
|
|
mv -i $LAYERS/commons/topo/v1/experimental/layers.aml \
|
| 978 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 979 |
|
|
mv -i $LAYERS/commons/topo/v1/experimental/aggregate.aml \
|
| 980 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 981 |
|
|
mv -i $LAYERS/commons/topo/v1/experimental/multiscalesmooth9a_clean.aml \
|
| 982 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 983 |
|
|
mv -i $LAYERS/commons/topo/v1/experimental/tilemerge_oregon1.aml \
|
| 984 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 985 |
|
|
mv -i $LAYERS/commons/topo/v1/scripts/unpacktiles.aml \
|
| 986 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 987 |
|
|
mv -i $LAYERS/commons/topo/v1/scripts/unziptiles.py \
|
| 988 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 989 |
|
|
mv -i $LAYERS/commons/topo/v1/scripts/mrvbf/mrvbf6g-a3.aml \
|
| 990 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 991 |
|
|
mv -i $LAYERS/commons/topo/v1/scripts/mrvbf/pctl.aml \
|
| 992 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 993 |
|
|
mv -i $LAYERS/commons/topo/v1/scripts/mrvbf/chunkproc.aml \
|
| 994 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 995 |
|
|
mv -i $LAYERS/commons/topo/v1/scripts/mrvbf/pctl-limits.aml \
|
| 996 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 997 |
|
|
mv -i $LAYERS/commons/topo/v1/scripts/mrvbf/gauss3 \
|
| 998 |
|
|
$REPO/terrain/research/oregon/arcgis/v1/
|
| 999 |
|
|
# for now keep this mysterioud Windows binary around...
|
| 1000 |
|
|
mv -i $LAYERS/commons/topo/v1/scripts/mrvbf/pctl.exe \
|
| 1001 |
|
|
$LAYERS/commons/topo/v1/
|
| 1002 |
|
|
# remove now-empty scripts directory
|
| 1003 |
|
|
rmdir $LAYERS/commons/topo/v1/scripts/mrvbf
|
| 1004 |
|
|
rmdir $LAYERS/commons/topo/v1/scripts
|
| 1005 |
|
|
|
| 1006 |
|
|
# consolidate second set of scripts into git repo
|
| 1007 |
|
|
mv -i $LAYERS/commons/topo/v2/experimental/layers.aml \
|
| 1008 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1009 |
|
|
mv -i $LAYERS/commons/topo/v2/experimental/aggregate.aml \
|
| 1010 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1011 |
|
|
mv -i $LAYERS/commons/topo/v2/experimental/multiscalesmooth9a_clean.aml \
|
| 1012 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1013 |
|
|
mv -i $LAYERS/commons/topo/v2/experimental/tilemerge_oregon1.aml \
|
| 1014 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1015 |
|
|
mv -i $LAYERS/commons/topo/v2/scripts/unpacktiles.aml \
|
| 1016 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1017 |
|
|
mv -i $LAYERS/commons/topo/v2/scripts/unziptiles.py \
|
| 1018 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1019 |
|
|
mv -i $LAYERS/commons/topo/v2/topo/mrvbf6g-a3.aml \
|
| 1020 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1021 |
|
|
mv -i $LAYERS/commons/topo/v2/topo/pctl.aml \
|
| 1022 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1023 |
|
|
mv -i $LAYERS/commons/topo/v2/topo/chunkproc.aml \
|
| 1024 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1025 |
|
|
mv -i $LAYERS/commons/topo/v2/topo/pctl-limits.aml \
|
| 1026 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1027 |
|
|
mv -i $LAYERS/commons/topo/v2/topo/gauss3 \
|
| 1028 |
|
|
$REPO/terrain/research/oregon/arcgis/v2/
|
| 1029 |
|
|
|
| 1030 |
6cc19306
|
Jim Regetz
|
|
| 1031 |
|
|
#
|
| 1032 |
|
|
# temp_benoit
|
| 1033 |
|
|
#
|
| 1034 |
|
|
|
| 1035 |
|
|
# for now just migrate to experimental area
|
| 1036 |
f3cc83bd
|
Jim Regetz
|
mv $ORGANISMS/temp_benoit $LAYERS/commons/
|
| 1037 |
6cc19306
|
Jim Regetz
|
|
| 1038 |
|
|
|
| 1039 |
|
|
#=======================================================================
|
| 1040 |
|
|
# fix up permissions and ownership
|
| 1041 |
|
|
#=======================================================================
|
| 1042 |
|
|
|
| 1043 |
|
|
chgrp -R layers $LAYERS/data
|
| 1044 |
|
|
find $LAYERS/data -type f -exec chmod 640 {} \;
|
| 1045 |
|
|
find $LAYERS/data -type d -exec chmod g-s {} \;
|
| 1046 |
|
|
find $LAYERS/data -type d -exec chmod 750 {} \;
|
| 1047 |
7526fb1c
|
Jim Regetz
|
|
| 1048 |
|
|
|
| 1049 |
|
|
#=======================================================================
|
| 1050 |
|
|
# now migrate code into git repository clone
|
| 1051 |
|
|
#=======================================================================
|
| 1052 |
|
|
|
| 1053 |
|
|
# nunokawa terrain scripts
|
| 1054 |
|
|
mkdir terrain/research/gtopo30
|
| 1055 |
77ed568c
|
Jim Regetz
|
mv -i code/terrain/nunokawa-scripts/toProduceData/clipUSGS.r \
|
| 1056 |
|
|
$REPO/terrain/research/gtopo30/
|
| 1057 |
|
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/check.r \
|
| 1058 |
|
|
$REPO/terrain/tests/
|
| 1059 |
|
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/meanElv_OnlyN59.r
|
| 1060 |
|
|
$REPO/terrain/research/north-60/
|
| 1061 |
7526fb1c
|
Jim Regetz
|
rm code/terrain/nunokawa-scripts/toAnalyzeData/meanElv.r
|
| 1062 |
|
|
rm code/terrain/nunokawa-scripts/toAnalyzeData/Deltas.r~
|
| 1063 |
77ed568c
|
Jim Regetz
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/Deltas.r \
|
| 1064 |
|
|
$REPO/terrain/research/north-60/
|
| 1065 |
7526fb1c
|
Jim Regetz
|
rm code/terrain/nunokawa-scripts/toAnalyzeData/rmse_cor.r~
|
| 1066 |
77ed568c
|
Jim Regetz
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/rmse_cor.r \
|
| 1067 |
|
|
$REPO/terrain/research/north-60/
|
| 1068 |
7526fb1c
|
Jim Regetz
|
rm code/terrain/nunokawa-scripts/toAnalyzeData/slope.r~
|
| 1069 |
77ed568c
|
Jim Regetz
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/{aspect,slope}.r
|
| 1070 |
|
|
$REPO/terrain/research/north-60/
|
| 1071 |
|
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/negativeTable.r \
|
| 1072 |
|
|
$REPO/terrain/research/north-60/
|
| 1073 |
|
|
mv -i code/terrain/nunokawa-scripts/toProduceData/*.{r,r~} \
|
| 1074 |
|
|
$REPO/terrain/research/north-60/
|
| 1075 |
7526fb1c
|
Jim Regetz
|
|
| 1076 |
|
|
# robinson terrain scripts
|
| 1077 |
77ed568c
|
Jim Regetz
|
mv -i code/terrain/DEM_ProcessingScripts/Aster_CheckMosaicedTilesExtents.py \
|
| 1078 |
|
|
$REPO/terrain/tests/
|
| 1079 |
|
|
mv -i code/terrain/DEM_ProcessingScripts/CheckPixelValuesAtOverlapZones.txt \
|
| 1080 |
|
|
$REPO/terrain/tests/
|
| 1081 |
|
|
mv -i code/terrain/DEM_ProcessingScripts/Aster\&SRTM_* \
|
| 1082 |
|
|
$REPO/terrain/tests/
|
| 1083 |
|
|
mv -i code/terrain/DEM_ProcessingScripts/Gaussian_Blend.r \
|
| 1084 |
|
|
$REPO/terrain/procedures/
|
| 1085 |
|
|
mv -i terrain/tests/Aster\&SRTM_* \
|
| 1086 |
|
|
$REPO/terrain/procedures/
|
| 1087 |
|
|
mv -i code/terrain/DEM_ProcessingScripts/SRTM_ClipToN59to60.txt \
|
| 1088 |
|
|
$REPO/terrain/procedures/
|
| 1089 |
|
|
mv -i code/terrain/DEM_ProcessingScripts/Mosaicing_AllTiles_East\&WestHemispheres.txt \
|
| 1090 |
|
|
$REPO/terrain/procedures/
|
| 1091 |
|
|
mv -i code/terrain/DEM_ProcessingScripts/AsterMosaicingScripts \
|
| 1092 |
|
|
$REPO/terrain/procedures/
|
| 1093 |
7526fb1c
|
Jim Regetz
|
|
| 1094 |
|
|
# robinson land-cover check
|
| 1095 |
77ed568c
|
Jim Regetz
|
mv -i code/land-cover/CheckForNoDataValues_LandCoverFiles.txt \
|
| 1096 |
|
|
$REPO/land-cover/tests/
|
| 1097 |
7526fb1c
|
Jim Regetz
|
|
| 1098 |
|
|
# robinson/donoghue Oregon MODIS LST processing code
|
| 1099 |
|
|
mkdir climate/research/oregon
|
| 1100 |
|
|
mkdir climate/research/oregon/modis-lst
|
| 1101 |
77ed568c
|
Jim Regetz
|
mv -i code/climate/modis-lst-oregon/*.{r,R,py} \
|
| 1102 |
|
|
$REPO/climate/research/oregon/modis-lst/
|
| 1103 |
7526fb1c
|
Jim Regetz
|
|
| 1104 |
|
|
# misc old (authorless) climate code
|
| 1105 |
77ed568c
|
Jim Regetz
|
mv -i code/climate/cru_3.0_data_extract.r \
|
| 1106 |
|
|
$REPO/climate/procedures/
|
| 1107 |
|
|
mv -i code/climate/gdd-worldclim-tmean-map-algebra.txt \
|
| 1108 |
|
|
$REPO/climate/extra/
|
| 1109 |
|
|
|
| 1110 |
|
|
mv -i $LAYERS/code/terrain/R_files/AsterCheck_demAndnum.r \
|
| 1111 |
|
|
$REPO/terrain/test/
|
| 1112 |
|
|
mv -i $LAYERS/code/terrain/R_files/PctNoLand.r \
|
| 1113 |
|
|
$REPO/terrain/research/gtopo30/
|
| 1114 |
|
|
|
| 1115 |
|
|
# set all file permissions to 644 before committing
|
| 1116 |
|
|
find $REPO -type f -exec ^Cmod 644 {} \;
|
