dtarb · dtarb · Mar 28, 2021 · Nov 3, 2020 · Nov 3, 2020 · Nov 3, 2020
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 #################
 ## Eclipse
 
+.idea
 *.pydevproject
 .project
 .metadata

diff --git a/README.txt b/README.txt
@@ -8,15 +8,17 @@ For the latest release and detailed documentation please refer to the website: h
 Building on Linux
 -----------------
 Both make and Cmake options are available to accommodate different preferences and system demands
-Using make
-cd src
-make
+Using make:
+> cd TauDEM
+> mkdir bin
+> cd src
+> make
 The executables are written to bin directory
 
-Using Cmake
-cd src && mkdir build && cd build
-cmake ..
-make && make install
+Using Cmake:
+> cd src && mkdir build && cd build
+> cmake ..
+> make && make install
 The executables are written to /usr/local/taudem directory.  This can be changed at the second last line (following DESTINATION) if desired.
 
 Dependencies
@@ -28,6 +30,7 @@ On Linux dependencies can be tricky.  I've added the following scripts to help,
 GDAL:  GDAL.sh installs from GDAL source. You could also try
 apt-get install gdal-bin libgdal-dev
 apt-get install gdal-bin=2.1.3+dfsg-1~xenial2
+apt-get install libmpich-dev (on Bionic 18.04 LTS)
 
 C++: The script GCC.sh contains some commands I've used to get the required compiler.
 

diff --git a/bin/aread8 b/bin/aread8
diff --git a/bin/areadinf b/bin/areadinf
diff --git a/bin/catchhydrogeo b/bin/catchhydrogeo
diff --git a/bin/catchoutlets b/bin/catchoutlets
diff --git a/bin/connectdown b/bin/connectdown
diff --git a/bin/d8flowdir b/bin/d8flowdir
diff --git a/bin/d8flowpathextremeup b/bin/d8flowpathextremeup
diff --git a/bin/d8hdisttostrm b/bin/d8hdisttostrm
diff --git a/bin/d8vdisttostrm b/bin/d8vdisttostrm
diff --git a/bin/dinfavalanche b/bin/dinfavalanche
diff --git a/bin/dinfconclimaccum b/bin/dinfconclimaccum
diff --git a/bin/dinfdecayaccum b/bin/dinfdecayaccum
diff --git a/bin/dinfdistdown b/bin/dinfdistdown
diff --git a/bin/dinfdistup b/bin/dinfdistup
diff --git a/bin/dinfflowdir b/bin/dinfflowdir
diff --git a/bin/dinfrevaccum b/bin/dinfrevaccum
diff --git a/bin/dinftranslimaccum b/bin/dinftranslimaccum
diff --git a/bin/dinfupdependence b/bin/dinfupdependence
diff --git a/bin/dropanalysis b/bin/dropanalysis
diff --git a/bin/editraster b/bin/editraster
diff --git a/bin/flowdircond b/bin/flowdircond
diff --git a/bin/gagewatershed b/bin/gagewatershed
diff --git a/bin/gridnet b/bin/gridnet
diff --git a/bin/inunmap b/bin/inunmap
diff --git a/bin/lengtharea b/bin/lengtharea
diff --git a/bin/moveoutletstostrm b/bin/moveoutletstostrm
diff --git a/bin/peukerdouglas b/bin/peukerdouglas
diff --git a/bin/pitremove b/bin/pitremove
diff --git a/bin/retlimflow b/bin/retlimflow
diff --git a/bin/setregion b/bin/setregion
diff --git a/bin/sinmapsi b/bin/sinmapsi
diff --git a/bin/slopearea b/bin/slopearea
diff --git a/bin/slopearearatio b/bin/slopearearatio
diff --git a/bin/slopeavedown b/bin/slopeavedown
diff --git a/bin/streamnet b/bin/streamnet
diff --git a/bin/threshold b/bin/threshold
diff --git a/bin/twi b/bin/twi
diff --git a/doc/TauDEM53CommandLineGuide.pdf b/doc/TauDEM53CommandLineGuide.pdf
diff --git a/examples/Logan/LoganOutlet.dbf b/examples/Logan/LoganOutlet.dbf
diff --git a/examples/Logan/LoganOutlet.geojson b/examples/Logan/LoganOutlet.geojson
@@ -0,0 +1,8 @@
+{
+"type": "FeatureCollection",
+"name": "LoganOutlet",
+"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:EPSG::26912" } },
+"features": [
+{ "type": "Feature", "properties": { "Id": 0 }, "geometry": { "type": "Point", "coordinates": [ 434791.762310470396187, 4621609.43730350676924 ] } }
+]
+}
diff --git a/examples/Logan/LoganOutlet.sbn b/examples/Logan/LoganOutlet.sbn
diff --git a/examples/Logan/LoganOutlet.sbx b/examples/Logan/LoganOutlet.sbx
diff --git a/examples/Logan/LoganOutlet.shp b/examples/Logan/LoganOutlet.shp
diff --git a/examples/Logan/LoganOutlet.shp.xml b/examples/Logan/LoganOutlet.shp.xml
@@ -0,0 +1,3 @@
+<?xml version="1.0"?>
+<!--<!DOCTYPE metadata SYSTEM "http://www.esri.com/metadata/esriprof80.dtd">-->
+<metadata xml:lang="en"><Esri><CreaDate>20100327</CreaDate><CreaTime>14054800</CreaTime><SyncOnce>TRUE</SyncOnce><MetaID>{1C82CCC0-BD2C-4762-A648-F554FBF332A1}</MetaID></Esri><idinfo><citation><citeinfo><onlink Sync="TRUE">\\MOUSE\C$\Scratch\LoganStart\OutletCopywithlongnameerrreadarahjnaknelk</onlink></citeinfo></citation></idinfo><distInfo><distributor><distorTran><onLineSrc><linkage Sync="TRUE">file://\\MOUSE\C$\Scratch\LoganStart\OutletCopywithlongnameerrreadarahjnaknelk</linkage><protocol Sync="TRUE">Local Area Network</protocol></onLineSrc></distorTran></distributor></distInfo><dataqual><lineage><procstep><procdesc Sync="TRUE">Dataset copied.</procdesc><srcused Sync="TRUE">C:\Scratch\Logan\Outlet</srcused><procdate Sync="TRUE">20100327</procdate><proctime Sync="TRUE">13312800</proctime></procstep><procstep><procdesc Sync="TRUE">Dataset copied.</procdesc><srcused Sync="TRUE">C:\Scratch\Logan\OutletCopywithlongnameerrreadarahjnaknelk</srcused><procdate Sync="TRUE">20100327</procdate><proctime Sync="TRUE">14054800</proctime></procstep></lineage></dataqual></metadata>
diff --git a/examples/Logan/LoganOutlet.shx b/examples/Logan/LoganOutlet.shx
diff --git a/examples/Logan/LoganOutlet.wgs.geojson b/examples/Logan/LoganOutlet.wgs.geojson
@@ -0,0 +1,8 @@
+{
+"type": "FeatureCollection",
+"name": "LoganOutlet",
+"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } },
+"features": [
+{ "type": "Feature", "properties": { "Id": 0 }, "geometry": { "type": "Point", "coordinates": [ -111.784228758779406, 41.743629188805421 ] } }
+]
+}
diff --git a/examples/Logan/TauDEMRScript.r b/examples/Logan/TauDEMRScript.r
@@ -0,0 +1,172 @@
+#  R script to run TauDEM
+
+# Packages used
+# install rgdal
+# install raster
+# install shapefiles
+install.packages("rgdal")
+install.packages("raster")
+install.packages("shapefiles")
+
+# This also assumes that MPICH2 is properly installed on your machine and that TauDEM command line executables exist
+# MPICH2.  Obtain from http://www.mcs.anl.gov/research/projects/mpich2/
+# Install following instructions at http://hydrology.usu.edu/taudem/taudem5.0/downloads.html.  
+# It is important that you install this from THE ADMINISTRATOR ACCOUNT.
+
+# TauDEM command line executables.  
+# If on a PC download from http://hydrology.usu.edu/taudem/taudem5.0/downloads.html
+# The install package will install to c:\program files\taudem or c:\program files (x86)\taudem set a 
+# system path.  If you want to do this manually you can download the command line executables and place where you wish.
+# If on a different system, download the source code and compile for your system.
+
+library(raster)
+library(shapefiles)
+
+# Set working directory to your location
+setwd("C:/Users/dtarb/Scratch/Logan")
+
+z=raster("logan.tif")
+plot(z)
+
+# Pitremove
+system("mpiexec -n 8 pitremove -z logan.tif -fel loganfel.tif")
+fel=raster("loganfel.tif")
+plot(fel)
+
+
+# D8 flow directions
+system("mpiexec -n 8 D8Flowdir -p loganp.tif -sd8 logansd8.tif -fel loganfel.tif",show.output.on.console=F,invisible=F)
+p=raster("loganp.tif")
+plot(p)
+sd8=raster("logansd8.tif")
+plot(sd8)
+
+# Contributing area
+system("mpiexec -n 8 AreaD8 -p loganp.tif -ad8 loganad8.tif")
+ad8=raster("loganad8.tif")
+plot(log(ad8))
+zoom(log(ad8))
+
+
+# Grid Network 
+system("mpiexec -n 8 Gridnet -p loganp.tif -gord logangord.tif -plen loganplen.tif -tlen logantlen.tif")
+gord=raster("logangord.tif")
+plot(gord)
+zoom(gord)
+
+# DInf flow directions
+system("mpiexec -n 8 DinfFlowdir -ang loganang.tif -slp loganslp.tif -fel loganfel.tif",show.output.on.console=F,invisible=F)
+ang=raster("loganang.tif")
+plot(ang)
+slp=raster("loganslp.tif")
+plot(slp)
+
+
+# Dinf contributing area
+system("mpiexec -n 8 AreaDinf -ang loganang.tif -sca logansca.tif")
+sca=raster("logansca.tif")
+plot(log(sca))
+zoom(log(sca))
+
+# Threshold
+system("mpiexec -n 8 Threshold -ssa loganad8.tif -src logansrc.tif -thresh 100")
+src=raster("logansrc.tif")
+plot(src)
+zoom(src)
+
+# a quick R function to write a shapefile
+makeshape.r=function(sname="shape",n=1)
+{
+xy=locator(n=n)
+points(xy)
+
+#Point
+dd <- data.frame(Id=1:n,X=xy$x,Y=xy$y)
+ddTable <- data.frame(Id=c(1),Name=paste("Outlet",1:n,sep=""))
+ddShapefile <- convert.to.shapefile(dd, ddTable, "Id", 1)
+write.shapefile(ddShapefile, sname, arcgis=T)
+}
+
+makeshape.r("ApproxOutlets")
+
+# Move Outlets
+system("mpiexec -n 8 moveoutletstostreams -p loganp.tif -src logansrc.tif -o approxoutlets.shp -om Outlet.shp")
+outpt=read.shp("outlet.shp")
+approxpt=read.shp("ApproxOutlets.shp")
+
+plot(src)
+points(outpt$shp[2],outpt$shp[3],pch=19,col=2)
+points(approxpt$shp[2],approxpt$shp[3],pch=19,col=4)
+
+zoom(src)
+
+
+# Contributing area upstream of outlet
+system("mpiexec -n 8 Aread8 -p loganp.tif -o Outlet.shp -ad8 loganssa.tif")
+ssa=raster("loganssa.tif")
+plot(ssa) 
+
+
+# Threshold
+system("mpiexec -n 8 threshold -ssa loganssa.tif -src logansrc1.tif -thresh 2000")
+src1=raster("logansrc1.tif")
+plot(src1)
+zoom(src1)
+
+# Stream Reach and Watershed
+system("mpiexec -n 8 Streamnet -fel loganfel.tif -p loganp.tif -ad8 loganad8.tif -src logansrc1.tif -o outlet.shp -ord loganord.tif -tree logantree.txt -coord logancoord.txt -net logannet.shp -w loganw.tif")
+plot(raster("loganord.tif"))
+zoom(raster("loganord.tif"))
+plot(raster("loganw.tif"))
+
+# Plot streams using stream order as width
+snet=read.shapefile("logannet")
+ns=length(snet$shp$shp)
+for(i in 1:ns)
+{
+  lines(snet$shp$shp[[i]]$points,lwd=snet$dbf$dbf$Order[i])
+}
+
+# Peuker Douglas stream definition
+system("mpiexec -n 8 PeukerDouglas -fel loganfel.tif -ss loganss.tif")
+ss=raster("loganss.tif")
+plot(ss)
+zoom(ss)
+
+#  Accumulating candidate stream source cells
+system("mpiexec -n 8 Aread8 -p loganp.tif -o outlet.shp -ad8 loganssa.tif -wg loganss.tif")
+ssa=raster("loganssa.tif")
+plot(ssa)
+
+#  Drop Analysis
+system("mpiexec -n 8 Dropanalysis -p loganp.tif -fel loganfel.tif -ad8 loganad8.tif -ssa loganssa.tif -drp logandrp.txt -o outlet.shp -par 5 500 10 0")
+
+# Deduce that the optimal threshold is 300 
+# Stream raster by threshold
+system("mpiexec -n 8 Threshold -ssa loganssa.tif -src logansrc2.tif -thresh 300")
+plot(raster("logansrc2.tif"))
+
+# Stream network
+system("mpiexec -n 8 Streamnet -fel loganfel.tif -p loganp.tif -ad8 loganad8.tif -src logansrc2.tif -ord loganord2.tif -tree logantree2.dat -coord logancoord2.dat -net logannet2.shp -w loganw2.tif -o Outlet.shp",show.output.on.console=F,invisible=F)
+
+plot(raster("loganw2.tif"))
+snet=read.shapefile("logannet2")
+ns=length(snet$shp$shp)
+for(i in 1:ns)
+{
+  lines(snet$shp$shp[[i]]$points,lwd=snet$dbf$dbf$Order[i])
+}
+
+# Wetness Index
+system("mpiexec -n 8 SlopeAreaRatio -slp loganslp.tif -sca logansca.tif -sar logansar.tif", show.output.on.console=F, invisible=F)
+sar=raster("logansar.tif")
+wi=sar
+wi[,]=-log(sar[,])
+plot(wi)
+
+# Distance Down
+system("mpiexec -n 8 DinfDistDown -ang loganang.tif -fel loganfel.tif -src logansrc2.tif -m ave v -dd logandd.tif",show.output.on.console=F,invisible=F)
+plot(raster("logandd.tif"))
+
+
+
diff --git a/examples/Logan/logan.aux b/examples/Logan/logan.aux
diff --git a/examples/Logan/logan.tif b/examples/Logan/logan.tif
diff --git a/examples/Logan/logan.tif.xml b/examples/Logan/logan.tif.xml
@@ -0,0 +1,3 @@
+<?xml version="1.0"?>
+<!--<!DOCTYPE metadata SYSTEM "http://www.esri.com/metadata/esriprof80.dtd">-->
+<metadata xml:lang="en"><Esri><MetaID>{04677E34-8EE2-4BAD-A9B6-854030986096}</MetaID><CreaDate>20100523</CreaDate><CreaTime>06561500</CreaTime><SyncOnce>TRUE</SyncOnce><DataProperties><lineage><Process ToolSource="C:\Program Files\ArcGIS\ArcToolbox\Toolboxes\Data Management Tools.tbx\CalculateStatistics" Date="20100523" Time="065615">CalculateStatistics C:\Scratch\Logan\logan.tif 1 1 # C:\Scratch\Logan\logan.tif</Process></lineage></DataProperties></Esri></metadata>