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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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#=======================================================================
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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 other cruft that i'm not quite ready to delete
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mkdir $LAYERS/cruft
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# create (temporary?) home for everything else
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mkdir $LAYERS/experimental
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mkdir $LAYERS/experimental/terrain
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mkdir $LAYERS/experimental/land-cover
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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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#
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# ASTER GDEM2
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#
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# remove gdal-generated metadata files
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rm $ORGANISMS/DEM/asterGdem2/*.aux.xml
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rm $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset/*.aux.xml
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rm $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset/Mosaiced/N59to60/*.aux.xml
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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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# ASTER GDEM1
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#
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#TODO
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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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mkdir $LAYERS/experimental/terrain/dem-cded
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# ... vrt files, what the heck
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mv -i $ORGANISMS/DEM/CanadaDED/*demFile.vrt \
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$LAYERS/experimental/terrain/dem-cded/
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# ... misc scripts and log files
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mv -i $ORGANISMS/DEM/CanadaDED/in*DemFile.txt \
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$LAYERS/experimental/terrain/dem-cded/
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mv -i $ORGANISMS/DEM/CanadaDED/unzipFiles.sh \
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$LAYERS/experimental/terrain/dem-cded/unzipFiles_0.sh
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/unzipFiles.sh \
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$LAYERS/experimental/terrain/dem-cded/unzipFiles_1.sh
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mv -i $ORGANISMS/DEM/CanadaDED/{.,/Monday}/*.sh \
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$LAYERS/experimental/terrain/dem-cded/
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mv -i $ORGANISMS/DEM/CanadaDED/*.log \
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$LAYERS/experimental/terrain/dem-cded/
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mv -i $ORGANISMS/DEM/CanadaDED/moscomps \
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$LAYERS/experimental/terrain/dem-cded/
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/filesToMosaic \
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$LAYERS/experimental/terrain/dem-cded/
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/*Log \
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$LAYERS/experimental/terrain/dem-cded/
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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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# cd $LAYERS/data/terrain/dem-cded-zip && ls \
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# | xargs -I+ sh -c 'unzip -l + | grep -e " 200[7-9]-"' \
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# | awk '{print $4}' > /home/layers/cded-extracts.txt
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# # ----- R code -----#
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# # read in the extracted file names
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# extracts <- scan("/home/layers/cded-extracts.txt", what="")
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# # read in all CDED files stored in the organisms home dir
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# files <- list.files(path=c("/home/organisms/DEM/CanadaDED",
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# "/home/organisms/DEM/CanadaDED/Monday"))
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# # note that all zip contents had been extracted (...based on filename)
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# all(extracts %in% files)
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# ## [1] TRUE
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# # isolate files *not* extracted from the zips
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# others <- setdiff(files, extracts)
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# # show that all extracted filenames match one of two patterns
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# all(grepl("dem$", extracts) | grepl("_fgdc_", extracts))
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# ## [1] TRUE
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# # and show that no other files match these
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# any(grepl("dem$", others) | grepl("_fgdc_", others))
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# ## [1] FALSE
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# # ------------------#
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rm $ORGANISMS/DEM/CanadaDED/*.dem
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rm $ORGANISMS/DEM/CanadaDED/*_fgdc_*.{xml,html}
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rm $ORGANISMS/DEM/CanadaDED/Monday/*.dem
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rm $ORGANISMS/DEM/CanadaDED/Monday/*_fgdc_*.{xml,html}
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# now remove items of uncertain origin
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rm $ORGANISMS/DEM/CanadaDED/*.dem.aux.xml
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rm $ORGANISMS/DEM/CanadaDED/Monday/*.dem.aux.xml
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rm $ORGANISMS/DEM/CanadaDED/*dem?.{aux,rrd}
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rm $ORGANISMS/DEM/CanadaDED/Monday/*dem?.{aux,rrd}
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rm $ORGANISMS/DEM/CanadaDED/*demFile.{aux,rrd,vrt.aux,tif.aux.xml,tif,vrt.rrd}
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rm $ORGANISMS/DEM/CanadaDED/CDEMPlySRTMDf.aux
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rm -r $ORGANISMS/DEM/CanadaDED/cdemplysrtmdf
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rm -r $ORGANISMS/DEM/CanadaDED/info
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# what the hell, remove other generated tifs because I really can't account for
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# the details of their creation...
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rm $ORGANISMS/DEM/CanadaDED/CanadaDemMos*.{tif,rrd,aux,aux.xml,tif.xml,img,vat.dbf}
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rm $ORGANISMS/DEM/CanadaDED/mergeCanada104105.{tif,aux,rrd}
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# remove now-empty directories
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rmdir $ORGANISMS/DEM/CanadaDED/Monday
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rmdir $ORGANISMS/DEM/CanadaDED
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#
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# FUSED DEM
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#
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# remove gdal-generated metadata files
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rm $ORGANISMS/DEM/GlobalProduct/*.aux.xml
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# migrate to ~layers
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mv $ORGANISMS/DEM/GlobalProduct $LAYERS/data/terrain/dem-fused
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#
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# GTOPO30
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#
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# remove gdal-generated metadata file
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rm $ORGANISMS/DEM/usgsGTOPO30/e020n90/*.aux.xml
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# now migrate to ~layers
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mv $ORGANISMS/DEM/usgsGTOPO30 $LAYERS/data/terrain/dem-usgs-gtopo30
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#
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# GMTED2010
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#
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245
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# remove gdal-generated metadata files
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rm $ORGANISMS/GMTED2010/*.aux.xml
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248
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# remove ArcMap(?) schema lock file
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249
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rm $ORGANISMS/GMTED2010/GMTED2010_Spatial_Metadata/GMTED2010_Spatial_Metadata.shp.IGSKMNCNWK00726.6284.8844.sr.lock
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# migrate original (I think) downloaded data (OR only)
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mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-tiles
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mv $ORGANISMS/GMTED2010/30N150W_20101117_gmted_mea300.tif \
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$LAYERS/data/terrain/dem-gmted2010-mea300-OR-tiles/
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mv $ORGANISMS/GMTED2010/30N120W_20101117_gmted_mea300.tif \
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$LAYERS/data/terrain/dem-gmted2010-mea300-OR-tiles/
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256
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# migrate merged OR tiles (i think)
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257
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mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-mosaic
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mv $ORGANISMS/GMTED2010/OR_Coverage.tif \
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$LAYERS/data/terrain/dem-gmted2010-mea300-OR-mosaic/
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# migrate OR clipped/reprojected data
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261
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mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-tif
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mv $ORGANISMS/GMTED2010/OR_ClippedToMODIS_InSinu.tif \
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$LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-tif/
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264
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mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-bil
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mv $ORGANISMS/GMTED2010/OR_ClippedToMODIS_InSinu.{prj,hdr,bil} \
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$LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-bil/
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267
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# migrate shapefile
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268
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mv $ORGANISMS/GMTED2010/GMTED2010_Spatial_Metadata \
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$LAYERS/data/terrain/dem-gmted2010-spatial-metadata
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270
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# migrate documentation
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mv $ORGANISMS/GMTED2010/of2011-1073.pdf $LAYERS/documentation/terrain/gmted2010-report.pdf
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272
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mv $ORGANISMS/GMTED2010/ReadMe $LAYERS/documentation/terrain/gmted2010-readme.txt
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273
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# remove now-empty directory
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274
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rmdir $ORGANISMS/GMTED2010
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275
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276
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#
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277
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# Nunokawa content
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278
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#
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279
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280
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# TODO: deal with data
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281
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_82N.tif # Int16 59N-82N GDEM2 elevation
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282
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_below.tif # Int16 59N-60N GDEM2 elevation
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283
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_above.tif # Int16 60N-61N GDEM2 elevation
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284
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_straddle.tif # Int16 59N-61N GDEM2 elevation (GDEM2 above, GDEM2 below)
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285
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_straddle_a.tif # Flt32 59N-61N GDEM2-based aspect
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286
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_straddle_s.tif # Flt32 59N-61N GDEM2-based slope
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287
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_below_blendgau.tif # Flt32 59N-60N GDEM2/SRTM blended elevation
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288
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289
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$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_straddle.tif # Int16 59N-61N GDEM2/SRTM unblended elevation (GDEM2 above, SRTM below)
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290
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$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_straddle_a.tif # Flt32 59N-61N unblended-based aspect
|
|
291
|
$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_straddle_s.tif # Flt32 59N-61N unblended-based aspect
|
|
292
|
|
|
293
|
$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_blendgau.tif # Int16 59N-61N GDEM2/SRTM blended elevation (GDEM2 above, blended below)
|
|
294
|
$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_blendgau_a.tif # Flt32 59N-61N blend-based aspect
|
|
295
|
$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_blendgau_s.tif # Flt32 59N-61N blend-based aspect
|
|
296
|
|
|
297
|
$ORGANISMS/DEM/Yuni/Data/srtm/srtm_*_below.tif # Int16 59N-60N SRTM elevation
|
|
298
|
$ORGANISMS/DEM/Yuni/Data/srtm/srtm_*_below_a.tif # Flt32 59N-60N SRTM-based aspect
|
|
299
|
$ORGANISMS/DEM/Yuni/Data/srtm/srtm_*_below_below_s.tif # Flt32 59N-60N SRTM-based slope
|
|
300
|
|
|
301
|
$ORGANISMS/DEM/Yuni/Data/aster2/aster.vrt # VRT - GDEM2 from ~59N-82N (with 1/2-pixel offset)
|
|
302
|
$ORGANISMS/DEM/Yuni/Data/srtm/srtm.vrt # VRT - SRTM from ~55N-60N (with 1/2-pixel offset)
|
|
303
|
|
|
304
|
$ORGANISMS/DEM/Yuni/Data/GTOPO30/*.dem # 59N-~82N GTOPO30 elevation clipped
|
|
305
|
|
|
306
|
# remove duplicate file
|
|
307
|
rm $ORGANISMS/DEM/Yuni/Data/aster2/fused_w180w141
|
|
308
|
# remove redundant backup files (but leaving some others)
|
|
309
|
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/aspect.r~
|
|
310
|
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/check.r~
|
|
311
|
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/meanElv.r~
|
|
312
|
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/meanElv_onlyN59.r~
|
|
313
|
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/
|
|
314
|
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/assembling.r~
|
|
315
|
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/gaussian.r~
|
|
316
|
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/mkVrt_Tiff.r~
|
|
317
|
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/slope_aspect.r~
|
|
318
|
# migrate scripts files
|
|
319
|
mv $ORGANISMS/DEM/Yuni/scripts \
|
|
320
|
$LAYERS/code/terrain/nunokawa-scripts
|
|
321
|
# migrate documents
|
|
322
|
mv -i $ORGANISMS/DEM/Yuni/documents \
|
|
323
|
$LAYERS/documentation/terrain/nunokawa-documents
|
|
324
|
mv -i $ORGANISMS/DEM/Yuni/missing_gdem2_tiles.txt \
|
|
325
|
$LAYERS/documentation/terrain/nunokawa-documents/
|
|
326
|
mv -i $ORGANISMS/DEM/Yuni/metadata.txt \
|
|
327
|
$LAYERS/documentation/terrain/nunokawa-documents/
|
|
328
|
|
|
329
|
#
|
|
330
|
# Remaining DEM content
|
|
331
|
#
|
|
332
|
|
|
333
|
mv $ORGANISMS/DEM/DEM_ProcessingScripts $LAYERS/code/terrain/
|
|
334
|
mv $ORGANISMS/DEM/ReadMeInProgress.txt $LAYERS/documentation/terrain/misc-partial-readme.txt
|
|
335
|
|
|
336
|
|
|
337
|
rm $ORGANISMS/DEM/checklog
|
|
338
|
mv $ORGANISMS/DEM/checkBadAsterGDEMFiles.sh $LAYERS/cruft/
|
|
339
|
mv $ORGANISMS/DEM/CheckGDEMLog.txt $LAYERS/cruft/
|
|
340
|
|
|
341
|
|
|
342
|
#=========#
|
|
343
|
# CLIMATE #
|
|
344
|
#=========#
|
|
345
|
|
|
346
|
#
|
|
347
|
# CRU
|
|
348
|
#
|
|
349
|
|
|
350
|
# migrate original gz data from CRU (or so it appears...)
|
|
351
|
mkdir $LAYERS/data/climate/cru-ts-3.0-1901-2006-gzip
|
|
352
|
mv $ORGANISMS/CRU_TS_3.0/*.gz $LAYERS/data/climate/cru-ts-3.0-1901-2006-gzip/
|
|
353
|
# I confirmed that the gunzipped files are identical to the gz contents (by
|
|
354
|
# gunzipping to /tmp and then diffing):w
|
|
355
|
# ...so let's delete the uncompressed versions
|
|
356
|
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.pre.nc
|
|
357
|
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.tmn.nc
|
|
358
|
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.tmp.nc
|
|
359
|
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.tmx.nc
|
|
360
|
# migrate extracted ASCII grid files
|
|
361
|
mv $ORGANISMS/CRU_TS_3.0/PRE $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-pre
|
|
362
|
mv $ORGANISMS/CRU_TS_3.0/TMN $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-tmn
|
|
363
|
mv $ORGANISMS/CRU_TS_3.0/TMP $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-tmp
|
|
364
|
mv $ORGANISMS/CRU_TS_3.0/TMX $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-tmx
|
|
365
|
# migrate R script for asc extraction
|
|
366
|
mv -i $ORGANISMS/CRU_TS_3.0/R/cru_3.0_data_extract.r $LAYERS/code/climate/
|
|
367
|
# rename then migrate readmes
|
|
368
|
rename 's/(Read_Me)/clim-cru-ts-3.0-\1/' $ORGANISMS/CRU_TS_3.0/Read_Me_*.txt
|
|
369
|
mv $ORGANISMS/CRU_TS_3.0/*Read_Me_*.txt $LAYERS/documentation/climate/
|
|
370
|
# now remove empty directory structure
|
|
371
|
find $ORGANISMS/CRU_TS_3.0 -depth -type d -exec rmdir {} \;
|
|
372
|
|
|
373
|
#
|
|
374
|
# GSOD
|
|
375
|
#
|
|
376
|
|
|
377
|
# for now, just move the whole thing as-is
|
|
378
|
mv $ORGANISMS/gsod $LAYERS/data/climate/gsod
|
|
379
|
|
|
380
|
#
|
|
381
|
# GHCN
|
|
382
|
#
|
|
383
|
|
|
384
|
# for now, just move the whole thing as-is
|
|
385
|
mv $ORGANISMS/ghcn $LAYERS/data/climate/ghcn
|
|
386
|
|
|
387
|
#
|
|
388
|
# MODIS LST
|
|
389
|
#
|
|
390
|
|
|
391
|
# migrate MOD11A1 V4 daily 1km L3 LST (March 1-7, 2000)
|
|
392
|
mv $ORGANISMS/MODIS\ LST/MOD11A1.004 $LAYERS/data/climate/MOD11A1.004-daily-1km-L3-LST/
|
|
393
|
# migrate MOD11A2 V4 8-day 1km L3 LST (March 5, 2000)
|
|
394
|
mkdir $LAYERS/data/climate/MOD11A2.004-8day-1km-L3-LST
|
|
395
|
mv $ORGANISMS/MODIS\ LST/2000.03.05 $LAYERS/data/climate/MOD11A2.004-8day-1km-L3-LST/
|
|
396
|
# also remove identical copies of the MOD11A2 data (confirmed by diffing)
|
|
397
|
rm $ORGANISMS/Modis_2000.03.05/MOD11A2.A2000065.*.hdf
|
|
398
|
rm $ORGANISMS/Modis_2000.03.05/MOD11A2.A2000065.*.hdf.xml
|
|
399
|
rmdir $ORGANISMS/Modis_2000.03.05
|
|
400
|
# remove now-empty directory
|
|
401
|
rmdir $ORGANISMS/MODIS\ LST
|
|
402
|
|
|
403
|
#
|
|
404
|
# MODIS LST -- Oregon
|
|
405
|
#
|
|
406
|
|
|
407
|
# migrate original MODIS OR hdfs (2001-2010?)
|
|
408
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-orig
|
|
409
|
mv $ORGANISMS/MODIS_LST_Oregon/MOD11A1.*.hdf \
|
|
410
|
$LAYERS/data/climate/MOD11A1.004-OR-orig/
|
|
411
|
mv $ORGANISMS/MODIS_LST_Oregon/MOD11A1.*.hdf.xml \
|
|
412
|
$LAYERS/data/climate/MOD11A1.004-OR-orig/
|
|
413
|
# migrate original MODIS OR hdfs (2000, not used)
|
|
414
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-orig-2000
|
|
415
|
mv $ORGANISMS/MODIS_LST_Oregon/2000\ _WithheldFromAVG/MOD11A1.A2000*.hdf \
|
|
416
|
$LAYERS/data/climate/MOD11A1.004-OR-orig-2000/
|
|
417
|
mv $ORGANISMS/MODIS_LST_Oregon/2000\ _WithheldFromAVG/MOD11A1.A2000*.hdf.xml \
|
|
418
|
$LAYERS/data/climate/MOD11A1.004-OR-orig-2000/
|
|
419
|
# migrate ClearDayCov OR img extracts (2001-2010?)
|
|
420
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img
|
|
421
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/MOD11A1.*.img \
|
|
422
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img/
|
|
423
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/MOD11A1.*.img.aux.xml \
|
|
424
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img/
|
|
425
|
# migrate ClearDayCov OR img extracts (2000, not used)
|
|
426
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-2000
|
|
427
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/2000_WithheldFromAVG/MOD11A1.A2000*.005_ClearDay.img \
|
|
428
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-2000/
|
|
429
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/2000_WithheldFromAVG/MOD11A1.A2000*.005_ClearDay.img.aux.xml \
|
|
430
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-2000/
|
|
431
|
|
|
432
|
# migrate renamed ClearDayCov OR img extracts (2001-2010?)
|
|
433
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed
|
|
434
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/*.img \
|
|
435
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed/
|
|
436
|
# migrate renamed ClearDayCov OR img extracts (2000, not used)
|
|
437
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-2000
|
|
438
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/2000_WithheldFromAVG/MOD11A1.A.2000.*.img \
|
|
439
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-2000/
|
|
440
|
|
|
441
|
# migrate renamed ClearDayCov OR img extracts with corrected pixels
|
|
442
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-fixed
|
|
443
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/*.img \
|
|
444
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-fixed/
|
|
445
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/*.img.aux.xml \
|
|
446
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-fixed/
|
|
447
|
|
|
448
|
# migrate ClearDayCov OR daily avg tiles
|
|
449
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img
|
|
450
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day*.img \
|
|
451
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img/
|
|
452
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day*.img.aux.xml \
|
|
453
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img/
|
|
454
|
# migrate ClearDayCov OR daily avg mosaic imgs
|
|
455
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img
|
|
456
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.img \
|
|
457
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img
|
|
458
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.img.aux.xml \
|
|
459
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img
|
|
460
|
# migrate ClearDayCov OR daily avg mosaic bils
|
|
461
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil
|
|
462
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.prj \
|
|
463
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/
|
|
464
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.bil \
|
|
465
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/
|
|
466
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.bil.aux.xml \
|
|
467
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/
|
|
468
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.hdr \
|
|
469
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/
|
|
470
|
|
|
471
|
# migrate ClearDayCov OR monthly avg tiles
|
|
472
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-tiles-img
|
|
473
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/*_AVG_Scaled.img \
|
|
474
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-tiles-img/
|
|
475
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/*_AVG_Scaled.img.aux.xml \
|
|
476
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-tiles-img/
|
|
477
|
# migrate ClearDayCov OR monthly avg mosaic imgs
|
|
478
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-img
|
|
479
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.img \
|
|
480
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-img/
|
|
481
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.img.aux.xml \
|
|
482
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-img/
|
|
483
|
# migrate ClearDayCov OR monthly avg mosaic bils
|
|
484
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil
|
|
485
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.prj \
|
|
486
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/
|
|
487
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.bil \
|
|
488
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/
|
|
489
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.bil.aux.xml \
|
|
490
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/
|
|
491
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.hdr \
|
|
492
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/
|
|
493
|
|
|
494
|
# migrate *old* (wrong?) ClearDayCov OR daily avg tiles
|
|
495
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD
|
|
496
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Tiles_Old/Day_*_Average_Scaled_*.img \
|
|
497
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD/
|
|
498
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Tiles_Old/Day_*_Average_Scaled_*.img.aux.xml \
|
|
499
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD/
|
|
500
|
# migrate *old* (wrong?) ClearDayCov OR daily avg mosaics
|
|
501
|
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img-OLD
|
|
502
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Mosaic_Old/Day_*_ClearDay_Average.img \
|
|
503
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img-OLD/
|
|
504
|
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Mosaic_Old/Day_*_ClearDay_Average.img.aux.xml \
|
|
505
|
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img-OLD/
|
|
506
|
|
|
507
|
# remove identical copies of (old) ClearDayCov daily avgs for tile h08v04
|
|
508
|
# *Note*: I first confirmed that these are duplicate copies:
|
|
509
|
# for i in {1..366};
|
|
510
|
# do
|
|
511
|
# diff -q $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old/Day_"$i"_Average_Scaled.img \
|
|
512
|
# $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD/Day_"$i"_Average_Scaled_h08v04.img
|
|
513
|
# done
|
|
514
|
rm $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old/Day_{1..366}_Average_Scaled.img
|
|
515
|
rm $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old/Day_{1..366}_Average_Scaled.img.aux.xml
|
|
516
|
# remove now-empty directory
|
|
517
|
rmdir $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old
|
|
518
|
|
|
519
|
# remove misc bil statistics (stx) files)
|
|
520
|
rm $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day11_Mosaic_DailyAvg_Scaled.stx
|
|
521
|
rm $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day1_Mosaic_DailyAvg_Scaled.stx
|
|
522
|
rm $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/AprMosaic_MonthlyAvg_Scaled.stx
|
|
523
|
|
|
524
|
# remove pyc file
|
|
525
|
rm $ORGANISMS/MODIS_LST_Oregon/GDAL_Extract_ClearDay_from_HDF_Files.pyc
|
|
526
|
|
|
527
|
# move and (if needed) rename documentation files
|
|
528
|
mv -i $ORGANISMS/MODIS_LST_Oregon/1\ ReadMe\ First.txt \
|
|
529
|
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-orig-readme.txt
|
|
530
|
mv -i $ORGANISMS/MODIS_LST_Oregon/MODIS_Oregon_ProcessingInfo.doc \
|
|
531
|
$LAYERS/documentation/climate/
|
|
532
|
mv -i $ORGANISMS/MODIS_LST_Oregon/2000\ _WithheldFromAVG/ReadMe \
|
|
533
|
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-orig-2000-readme.txt
|
|
534
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/1\ ReadMe\ First.txt \
|
|
535
|
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-clearday-readme.txt
|
|
536
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/1\ ReadMe\ First \
|
|
537
|
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-clearday-img-renamed-fixed-readme.txt
|
|
538
|
|
|
539
|
# move scripts
|
|
540
|
mkdir $LAYERS/code/climate/modis-lst-oregon
|
|
541
|
mv -i $ORGANISMS/MODIS_LST_Oregon/GDAL_Extract_ClearDay_from_HDF_Files.py \
|
|
542
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
543
|
mv -i $ORGANISMS/MODIS_LST_Oregon/QCTagCheck \
|
|
544
|
$LAYERS/code/climate/modis-lst-oregon/QCTagCheck.py
|
|
545
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ConvertMODIStobil.py \
|
|
546
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
547
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/DayAVGCalcs_h08v04TIles.r \
|
|
548
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
549
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/DayAVGCalcs_h09v04TIles.r \
|
|
550
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
551
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/LST_Mosaicing_DailyAvgs.r \
|
|
552
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
553
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/LST_Mosaicing_MonthlyAvgs.R \
|
|
554
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
555
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/Conversion_hdf_to_img.py \
|
|
556
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
557
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/h09v04Tiles_BadPixelCorrection.r \
|
|
558
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
559
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/h08v04Tiles_BadPixelCorrection.r \
|
|
560
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
561
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/Convert\ MODIS\ Day\ of\ Year\ to\ Date\ File\ Name.py \
|
|
562
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
563
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/MonthlyAvgCalcs_h08v04Tiles.r \
|
|
564
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
565
|
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/MonthlyAvgCalcs_h09v04Tiles.r \
|
|
566
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
567
|
|
|
568
|
# move last few things...
|
|
569
|
mv -i $ORGANISMS/MODIS_LST_Oregon/hdf.txt \
|
|
570
|
$LAYERS/cruft/clim-MOD11A1.004-OR-orig-hdf.txt
|
|
571
|
mv -i $ORGANISMS/MODIS_LST_Oregon/SDS_PctFills.txt \
|
|
572
|
$LAYERS/cruft/clim-MOD11A1.004-OR-orig-SDS_PctFills.txt
|
|
573
|
|
|
574
|
# remove all the now-empty directories...
|
|
575
|
# tree $ORGANISMS/MODIS_LST_Oregon
|
|
576
|
# /home/organisms/MODIS_LST_Oregon
|
|
577
|
# .
|
|
578
|
# ├── 2000 _WithheldFromAVG
|
|
579
|
# └── ClearDayGDAL
|
|
580
|
# ├── ClearDay_DailyAverage_Mosaic_Old
|
|
581
|
# ├── ClearDay_DailyAverage_Tiles_Old
|
|
582
|
# ├── ClearDay_Original_IMG_Extracts
|
|
583
|
# │  ├── 2000_WithheldFromAVG
|
|
584
|
# │  └── ByDate
|
|
585
|
# │  ├── 2000_WithheldFromAVG
|
|
586
|
# │  └── BadPixelsCorrected_Tiles
|
|
587
|
# ├── NewClearDay_DailyAvgs_Mosaics
|
|
588
|
# ├── NewClearDay_DailyAvgs_Tiles
|
|
589
|
# ├── NewClearDay_MonthlyAvgs_Mosaics
|
|
590
|
# └── NewClearDay_MonthlyAvgs_Tiles
|
|
591
|
find $ORGANISMS/MODIS_LST_Oregon -depth -type d -exec rmdir {} \;
|
|
592
|
|
|
593
|
# last but not least, deal with top level R directory
|
|
594
|
# ...move some (old? superceded?) scripts
|
|
595
|
mv -i $ORGANISMS/R/ReClass Clear Day Rasters h08v04.r \
|
|
596
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
597
|
mv -i $ORGANISMS/R/Calc Clear Day Daily Avg.r \
|
|
598
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
599
|
mv -i $ORGANISMS/R/Mosaic Clear Day Average Grids.r \
|
|
600
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
601
|
mv -i $ORGANISMS/R/Calc Clear Day Monthly Avg.r \
|
|
602
|
$LAYERS/code/climate/modis-lst-oregon/
|
|
603
|
# don't know how this was created, but it's clearly derived data...
|
|
604
|
mv -i $ORGANISMS/R/Modis_LSTdaily_climatology $LAYERS/data/clim-modis-lstdaily
|
|
605
|
# remove now-empty directory
|
|
606
|
rmdir $ORGANISMS/R
|
|
607
|
|
|
608
|
#
|
|
609
|
# TRMM
|
|
610
|
#
|
|
611
|
|
|
612
|
# this was an *empty* directory! removing...
|
|
613
|
rmdir $ORGANISMS/TRMM
|
|
614
|
|
|
615
|
#
|
|
616
|
# WorldClim
|
|
617
|
#
|
|
618
|
|
|
619
|
# migrate each one into its own directory
|
|
620
|
mkdir $LAYERS/data/climate/worldclim-bio-30s-esri-zip
|
|
621
|
mv $ORGANISMS/WorldClim/bio_30s_esri.zip $LAYERS/data/climate/worldclim-bio-30s-esri-zip/
|
|
622
|
mkdir $LAYERS/data/climate/worldclim-prec-30s-esri-zip
|
|
623
|
mv $ORGANISMS/WorldClim/prec_30s_esri.zip $LAYERS/data/climate/worldclim-prec-30s-esri-zip/
|
|
624
|
mkdir $LAYERS/data/climate/worldclim-tmax-30s-esri-zip
|
|
625
|
mv $ORGANISMS/WorldClim/tmax_30s_esri.zip $LAYERS/data/climate/worldclim-tmax-30s-esri-zip/
|
|
626
|
mkdir $LAYERS/data/climate/worldclim-tmean-30s-esri-zip
|
|
627
|
mv $ORGANISMS/WorldClim/tmean_30s_esri.zip $LAYERS/data/climate/worldclim-tmean-30s-esri-zip/
|
|
628
|
mkdir $LAYERS/data/climate/worldclim-tmin-30s-esri-zip
|
|
629
|
mv $ORGANISMS/WorldClim/tmin_30s_esri.zip $LAYERS/data/climate/worldclim-tmin-30s-esri-zip/
|
|
630
|
# remove now-empty directory
|
|
631
|
rmdir $ORGANISMS/WorldClim
|
|
632
|
|
|
633
|
|
|
634
|
#============#
|
|
635
|
# LAND COVER #
|
|
636
|
#============#
|
|
637
|
|
|
638
|
#
|
|
639
|
# GLCNMO
|
|
640
|
#
|
|
641
|
|
|
642
|
# for now, just move the whole thing as-is
|
|
643
|
mv $ORGANISMS/GLCNMO $LAYERS/experimental/land-cover/
|
|
644
|
|
|
645
|
#
|
|
646
|
# GlobCover
|
|
647
|
#
|
|
648
|
# migrate what seems like the original data (?)
|
|
649
|
mkdir $LAYERS/data/land-cover/GlobCover-v2.2
|
|
650
|
mv -i $ORGANISMS/GlobCoverv2.2/GLOBCOVER_200412_200606_V2.2_Global_CLA* \
|
|
651
|
$LAYERS/data/land-cover/GlobCover-v2.2/
|
|
652
|
# migrate mysterious derivatives of the above
|
|
653
|
mkdir $LAYERS/data/land-cover/GlobCover-v2.2-arcgis
|
|
654
|
mv -i $ORGANISMS/GlobCoverv2.2/globcov22_beh $LAYERS/data/land-cover/GlobCover-v2.2-arcgis/
|
|
655
|
mv -i $ORGANISMS/GlobCoverv2.2/globcoverv22 $LAYERS/data/land-cover/GlobCover-v2.2-arcgis/
|
|
656
|
# migrate reference info to documentation area
|
|
657
|
mv -i $ORGANISMS/GlobCoverv2.2/Globcover_* $LAYERS/documentation/land-cover/
|
|
658
|
# remove now-empty directory
|
|
659
|
rmdir $ORGANISMS/GlobCoverv2.2
|
|
660
|
|
|
661
|
#
|
|
662
|
# LandCover (whatever that is)
|
|
663
|
#
|
|
664
|
|
|
665
|
# remove gdal-generated metadata file
|
|
666
|
rm $ORGANISMS/LandCover/Layer10_Clip1.tif.aux.xml
|
|
667
|
# migrate original OR landcover tiles
|
|
668
|
mkdir $LAYERS/data/land-cover/lc-OR-tiles
|
|
669
|
mv $ORGANISMS/LandCover/Layer*_Clip[1-3].tif \
|
|
670
|
$LAYERS/data/land-cover/lc-OR-tiles/
|
|
671
|
# migrate OR landcover mosaics
|
|
672
|
mkdir $LAYERS/data/land-cover/lc-OR-mosaic
|
|
673
|
mv $ORGANISMS/LandCover/Layer*_Mosaic.tif \
|
|
674
|
$LAYERS/data/land-cover/lc-OR-mosaic/
|
|
675
|
# migrate OR clipped/reprojected landcover mosaics
|
|
676
|
mkdir $LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu
|
|
677
|
mv $ORGANISMS/LandCover/Layer*_ClippedToMODIS_Sinu.* \
|
|
678
|
$LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu/
|
|
679
|
# migrate OR multiband clipped/reprojected landcover mosaic
|
|
680
|
mkdir $LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu-multiband
|
|
681
|
mv $ORGANISMS/LandCover/Final_Multiband_SinuGrid.* \
|
|
682
|
$LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu-multiband/
|
|
683
|
# migrate documentation
|
|
684
|
mv $ORGANISMS/LandCover/ReadMe $LAYERS/documentation/land-cover/landcover-ReadMe.txt
|
|
685
|
mv $ORGANISMS/LandCover/LCT\ calculations.xlsx $LAYERS/documentation/land-cover/
|
|
686
|
mv $ORGANISMS/LandCover/landcover_method_v3.docx $LAYERS/documentation/land-cover/
|
|
687
|
# migrate scripts
|
|
688
|
mv $ORGANISMS/LandCover/CheckForNoDataValues_LandCoverFiles.txt $LAYERS/code/land-cover/
|
|
689
|
# remove now-empty directory
|
|
690
|
rmdir $ORGANISMS/LandCover
|
|
691
|
|
|
692
|
#
|
|
693
|
# Tree height
|
|
694
|
#
|
|
695
|
|
|
696
|
# migrate $ORGANISMS/Tree_height/Lefsky2010
|
|
697
|
mkdir $LAYERS/data/land-cover/treeheight-lefsky2010
|
|
698
|
mv $ORGANISMS/Tree_height/Lefsky2010/x2_080809_global.img \
|
|
699
|
$LAYERS/data/land-cover/treeheight-lefsky2010/
|
|
700
|
mv $ORGANISMS/Tree_height/Lefsky2010/p_080809_global.img* \
|
|
701
|
$LAYERS/data/land-cover/treeheight-lefsky2010/
|
|
702
|
# migrate associated publication do documentation area
|
|
703
|
mv $ORGANISMS/Tree_height/Lefsky2010/Lefsky\ et\ al.\ 2010\ GeoRLett.pdf \
|
|
704
|
$LAYERS/documentation/land-cover/treeheight-Lefsky2010-GeoRLett.pdf
|
|
705
|
# remove now-empty directory
|
|
706
|
rmdir $ORGANISMS/Tree_height/Lefsky2010
|
|
707
|
|
|
708
|
# migrate $ORGANISMS/Tree_height/Simard2011
|
|
709
|
mkdir $LAYERS/data/land-cover/treeheight-simard2011
|
|
710
|
mv $ORGANISMS/Tree_height/Simard2011/Simard_Pinto_3DGlobalVeg_JGR.tif \
|
|
711
|
$LAYERS/data/land-cover/treeheight-simard2011/
|
|
712
|
# remove gdal-generated metadata file
|
|
713
|
rm $ORGANISMS/Tree_height/Simard2011/Simard_Pinto_3DGlobalVeg_JGR.tif.aux.xml
|
|
714
|
# migrate clipped/reprojected file (bil)
|
|
715
|
mkdir $LAYERS/data/land-cover/treeheight-simard2011-OR-clip-proj-sinu-bil
|
|
716
|
mv $ORGANISMS/Tree_height/Simard2011/GlobalCanopy_ClippedToMODIS_InSinu.* \
|
|
717
|
$LAYERS/data/land-cover/treeheight-simard2011-OR-clip-proj-sinu-bil/
|
|
718
|
# migrate documentation
|
|
719
|
mv $ORGANISMS/Tree_height/Simard2011/SimardEtAl2011_GlobalTreeHeight_WithLIDAR.pdf \
|
|
720
|
$LAYERS/documentation/land-cover/treeheight-SimardEtAl_GlobalTreeHeight_WithLIDAR.pdf
|
|
721
|
mv $ORGANISMS/Tree_height/Simard2011/ReadMe \
|
|
722
|
$LAYERS/documentation/land-cover/treeheight-ReadMe.txt
|
|
723
|
# remove remaining files as per instructions from Natalie Robinson
|
|
724
|
rm $ORGANISMS/Tree_height/Simard2011/Test_Clip.tif
|
|
725
|
rm $ORGANISMS/Tree_height/Simard2011/GDALTranslate_test.*
|
|
726
|
rm $ORGANISMS/Tree_height/Simard2011/GDALTranslate_DT_int16.*
|
|
727
|
# remove now-empty directory
|
|
728
|
rmdir $ORGANISMS/Tree_height/Simard2011
|
|
729
|
|
|
730
|
# lastely, remove now-empty Tree_height directory
|
|
731
|
rmdir $ORGANISMS/Tree_height
|
|
732
|
|
|
733
|
|
|
734
|
#=================#
|
|
735
|
# Remaining stuff #
|
|
736
|
#=================#
|
|
737
|
|
|
738
|
#
|
|
739
|
# top level directory
|
|
740
|
#
|
|
741
|
|
|
742
|
# move top level notes
|
|
743
|
mv $ORGANISMS/Oregon_CaseStudy_FileProcessingInfo $LAYERS/documentation/
|
|
744
|
mv $ORGANISMS/ReProjection_To_MODIS $LAYERS/documentation/
|
|
745
|
mv $ORGANISMS/README.txt $LAYERS/documentation/organisms-homedir-readme.txt
|
|
746
|
mv $ORGANISMS/CHANGES.txt $LAYERS/documentation/organisms-homedir-changes.txt
|
|
747
|
# move old file extension summary
|
|
748
|
mv -i $ORGANISMS/file-extension-summary.txt $LAYERS/cruft/
|
|
749
|
|
|
750
|
#
|
|
751
|
# Desktop
|
|
752
|
#
|
|
753
|
|
|
754
|
# move MRT installer to cruft
|
|
755
|
mv $ORGANISMS/Desktop/MRT_download_Linux $LAYERS/cruft/
|
|
756
|
# remove orphaned bil metadata file
|
|
757
|
rm $ORGANISMS/Desktop/ASTER_Test.bil.aux.xml
|
|
758
|
# remove empty Desktop dir
|
|
759
|
rmdir $ORGANISMS/Desktop
|
|
760
|
|
|
761
|
#
|
|
762
|
# pyhdf
|
|
763
|
#
|
|
764
|
|
|
765
|
# move pyhdf package to cruft
|
|
766
|
mv $ORGANISMS/pyhdf $LAYERS/cruft/
|
|
767
|
|
|
768
|
#
|
|
769
|
# GIS/GDD
|
|
770
|
#
|
|
771
|
|
|
772
|
# confirmed that /tmean contains unzipped tmean, except there are additional
|
|
773
|
# aux files presumably autogenerated by Arc -- I'm find with deleting them
|
|
774
|
# # ---- bash code ---#
|
|
775
|
# cd /tmp && unzip $ORGANISMS/GIS/GDD/tmean_30s_esri.zip
|
|
776
|
# diff -qr /tmp/tmean /home/organisms/GIS/GDD/tmean_30s_esri/tmean/
|
|
777
|
# done
|
|
778
|
# # ------------------#
|
|
779
|
# delete the uncompressed tmean_30s_esri directory
|
|
780
|
rm -r $ORGANISMS/GIS/GDD/tmean_30s_esri
|
|
781
|
|
|
782
|
# confirmed that WorldClim zips are identical to what we already have elsewhere
|
|
783
|
# # ---- bash code ---#
|
|
784
|
# for var in {'prec','tmin','tmax','tmean','bio'}
|
|
785
|
# do
|
|
786
|
# diff -s $ORGANISMS/GIS/GDD/"$var"_30s_esri.zip \
|
|
787
|
# $LAYERS/data/climate/worldclim-"$var"-30s-esri-zip/*.zip
|
|
788
|
# done
|
|
789
|
# done
|
|
790
|
# # ------------------#
|
|
791
|
# delete the duplicate worldclim zips
|
|
792
|
rm $ORGANISMS/GIS/GDD/prec_30s_esri.zip
|
|
793
|
rm $ORGANISMS/GIS/GDD/tmin_30s_esri.zip
|
|
794
|
rm $ORGANISMS/GIS/GDD/tmax_30s_esri.zip
|
|
795
|
rm $ORGANISMS/GIS/GDD/tmean_30s_esri.zip
|
|
796
|
rm $ORGANISMS/GIS/GDD/bio_30s_esri.zip
|
|
797
|
|
|
798
|
# confirmed that all MODIS files here are identical to (though in fact they are
|
|
799
|
# only a subset of) what we already have elsewhere
|
|
800
|
# # ---- bash code ---#
|
|
801
|
# for dir in `ls $ORGANISMS/GIS/GDD/MOD11A1.004`
|
|
802
|
# do
|
|
803
|
# echo checking "$dir"...
|
|
804
|
# ls $ORGANISMS/GIS/GDD/MOD11A1.004/"$dir" \
|
|
805
|
# | xargs -I+ \
|
|
806
|
# diff -q $ORGANISMS/GIS/GDD/MOD11A1.004/"$dir"/+ \
|
|
807
|
# $LAYERS/data/climate/MOD11A1.004-daily-1km-L3-LST/"$dir"/+
|
|
808
|
# done
|
|
809
|
# # ------------------#
|
|
810
|
# delete the duplicate MODIS data
|
|
811
|
# note that the last 3 dirs were already empty...
|
|
812
|
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.01/MOD11A1.A2000*.{hdf,hdf.xml}
|
|
813
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.01
|
|
814
|
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.02/MOD11A1.A2000*.{hdf,hdf.xml}
|
|
815
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.02
|
|
816
|
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.03/MOD11A1.A2000*.{hdf,hdf.xml}
|
|
817
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.03
|
|
818
|
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.04/MOD11A1.A2000*.{hdf,hdf.xml}
|
|
819
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.04
|
|
820
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.05
|
|
821
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.06
|
|
822
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.07
|
|
823
|
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004
|
|
824
|
|
|
825
|
# migrate remaining text (script?) file
|
|
826
|
mv $ORGANISMS/GIS/GDD/map\ algebra.txt $LAYERS/code/climate/gdd-worldclim-tmean-map-algebra.txt
|
|
827
|
# remove empty directory
|
|
828
|
rmdir $ORGANISMS/GIS/GDD
|
|
829
|
|
|
830
|
#
|
|
831
|
# GIS/terrain
|
|
832
|
#
|
|
833
|
|
|
834
|
# remove empty test directory
|
|
835
|
rmdir $ORGANISMS/GIS/terrain/test
|
|
836
|
# for now just migrate everything else to experimental area
|
|
837
|
mv $ORGANISMS/GIS/terrain $LAYERS/experimental/terrain/arcgis
|
|
838
|
|
|
839
|
# remove empty directory
|
|
840
|
rmdir $ORGANISMS/GIS
|
|
841
|
|
|
842
|
#
|
|
843
|
# Oregon
|
|
844
|
#
|
|
845
|
|
|
846
|
# TODO
|
|
847
|
|
|
848
|
#
|
|
849
|
# steph
|
|
850
|
#
|
|
851
|
|
|
852
|
# delete as per verbal instructions from Stephanie Pau
|
|
853
|
rm -rf $ORGANISMS/steph
|
|
854
|
|
|
855
|
#
|
|
856
|
# topo
|
|
857
|
#
|
|
858
|
|
|
859
|
# for now just migrate to experimental area
|
|
860
|
mv $ORGANISMS/topo $LAYERS/experimental/
|
|
861
|
|
|
862
|
#
|
|
863
|
# temp_benoit
|
|
864
|
#
|
|
865
|
|
|
866
|
# for now just migrate to experimental area
|
|
867
|
mv $ORGANISMS/temp_benoit $LAYERS/experimental/
|
|
868
|
|
|
869
|
|
|
870
|
#=======================================================================
|
|
871
|
# fix up permissions and ownership
|
|
872
|
#=======================================================================
|
|
873
|
|
|
874
|
chgrp -R layers $LAYERS/data
|
|
875
|
find $LAYERS/data -type f -exec chmod 640 {} \;
|
|
876
|
find $LAYERS/data -type d -exec chmod g-s {} \;
|
|
877
|
find $LAYERS/data -type d -exec chmod 750 {} \;
|
|
878
|
|
|
879
|
|
|
880
|
#=======================================================================
|
|
881
|
# now migrate code into git repository clone
|
|
882
|
#=======================================================================
|
|
883
|
|
|
884
|
# nunokawa terrain scripts
|
|
885
|
mkdir terrain/research/gtopo30
|
|
886
|
mv -i code/terrain/nunokawa-scripts/toProduceData/clipUSGS.r terrain/research/gtopo30/
|
|
887
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/check.r terrain/tests/
|
|
888
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/meanElv_OnlyN59.r terrain/research/north-60/
|
|
889
|
rm code/terrain/nunokawa-scripts/toAnalyzeData/meanElv.r
|
|
890
|
rm code/terrain/nunokawa-scripts/toAnalyzeData/Deltas.r~
|
|
891
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/Deltas.r terrain/research/north-60/
|
|
892
|
rm code/terrain/nunokawa-scripts/toAnalyzeData/rmse_cor.r~
|
|
893
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/rmse_cor.r terrain/research/north-60/
|
|
894
|
rm code/terrain/nunokawa-scripts/toAnalyzeData/slope.r~
|
|
895
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/{aspect,slope}.r terrain/research/north-60/
|
|
896
|
mv -i code/terrain/nunokawa-scripts/toAnalyzeData/negativeTable.r terrain/research/north-60/
|
|
897
|
mv -i code/terrain/nunokawa-scripts/toProduceData/*.{r,r~} terrain/research/north-60/
|
|
898
|
|
|
899
|
# robinson terrain scripts
|
|
900
|
mv -i code/terrain/DEM_ProcessingScripts/Aster_CheckMosaicedTilesExtents.py terrain/tests/
|
|
901
|
mv -i code/terrain/DEM_ProcessingScripts/CheckPixelValuesAtOverlapZones.txt terrain/tests/
|
|
902
|
mv -i code/terrain/DEM_ProcessingScripts/Aster\&SRTM_* terrain/tests/
|
|
903
|
mv -i code/terrain/DEM_ProcessingScripts/Gaussian_Blend.r terrain/procedures/
|
|
904
|
mv -i terrain/tests/Aster\&SRTM_* terrain/procedures/
|
|
905
|
mv -i code/terrain/DEM_ProcessingScripts/SRTM_ClipToN59to60.txt terrain/procedures/
|
|
906
|
mv -i code/terrain/DEM_ProcessingScripts/Mosaicing_AllTiles_East\&WestHemispheres.txt terrain/procedures/
|
|
907
|
mv -i code/terrain/DEM_ProcessingScripts/AsterMosaicingScripts terrain/procedures/
|
|
908
|
|
|
909
|
# robinson land-cover check
|
|
910
|
mv -i code/land-cover/CheckForNoDataValues_LandCoverFiles.txt land-cover/tests/
|
|
911
|
|
|
912
|
# robinson/donoghue Oregon MODIS LST processing code
|
|
913
|
mkdir climate/research/oregon
|
|
914
|
mkdir climate/research/oregon/modis-lst
|
|
915
|
mv -i code/climate/modis-lst-oregon/*.{r,R,py} climate/research/oregon/modis-lst/
|
|
916
|
|
|
917
|
# misc old (authorless) climate code
|
|
918
|
mv -i code/climate/cru_3.0_data_extract.r climate/procedures/
|
|
919
|
mv -i code/climate/gdd-worldclim-tmean-map-algebra.txt climate/extra/
|
|
920
|
|
|
921
|
# TODO: set all file permissions to 644 before committing
|
