Merge pull request #4 from jdbcode/develop

Develop
jdbcode · Jul 26, 2016 · 366f6c5 · 366f6c5
2 parents 312dab5 + 92b83ac
commit 366f6c5
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Showing 6 changed files with 31 additions and 15 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: LandsatLinkr
 Title: Tools to spectrally link Landsat data
-Version: 0.3.4
-Date: 2016-07-07
+Version: 0.3.5
+Date: 2016-07-026
 Authors@R: c(person("Justin", "Braaten", email = "[email protected]", role = c("aut", "cre")),
     person("Warren", "Cohen", email = "[email protected]", role = "aut"),
     person("Zhiqiang", "Yang", email = "[email protected]", role = "aut"))

diff --git a/R/calibrate_and_composite.r b/R/calibrate_and_composite.r
@@ -18,7 +18,7 @@
 #' @export
 
 
-calibrate_and_composite = function(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index,outdir,runname,useareafile,doyears="all",order="none",overlap="mean", cores=2, process, overwrite=F ,startday, endday){
+calibrate_and_composite = function(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index,outdir,runname,useareafile,doyears="all",order="none",overlap="mean", cores=2, process, overwrite=F ,startday, endday, yearadj){
 
   #msscal
   if(1 %in% process ==T){
@@ -60,10 +60,10 @@ calibrate_and_composite = function(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,in
     if(index == "all"){
       index = c("tca", "tcb", "tcg", "tcw")
       outdir = c(file.path(outdir,"tca"),file.path(outdir,"tcb"),file.path(outdir,"tcg"),file.path(outdir,"tcw"))
-      for(i in 1:length(index)){mixel(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index[i],outdir[i],runname,useareafile,doyears="all",order="none",overlap=overlap, startday=startday, endday=endday)} #overlap="mean"
+      for(i in 1:length(index)){mixel(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index[i],outdir[i],runname,useareafile,doyears="all",order="none",overlap=overlap, startday=startday, endday=endday, yearadj=yearadj)} #overlap="mean"
     } else {
       outdir = file.path(outdir,index)
-      mixel(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index,outdir,runname,useareafile,doyears="all",order="none",overlap=overlap, startday=startday, endday=endday) #overlap="mean"
+      mixel(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index,outdir,runname,useareafile,doyears="all",order="none",overlap=overlap, startday=startday, endday=endday, yearadj=yearadj) #overlap="mean"
     }
     print(proc.time()-t)
   }  

diff --git a/R/mixel.r b/R/mixel.r
@@ -17,7 +17,7 @@
 #' @export
 
 
-mixel = function(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index,outdir,runname,useareafile,doyears="all",order="none",overlap="mean",startday,endday){
+mixel = function(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index,outdir,runname,useareafile,doyears="all",order="none",overlap="mean",startday,endday,yearadj=0){
 
   mixel_find = function(files, refimg){
     info = matrix(ncol = 4, nrow=length(files))
@@ -74,7 +74,7 @@ mixel = function(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index,outdir,runname
     file.rename(envixmlfile,bsqxmlfile)
   }
 
-  mixel_composite = function(outdir, imginfosub, runname, index, order, useareafile, overlap){
+  mixel_composite = function(outdir, imginfosub, runname, index, order, useareafile, overlap, yearadj){
 
     #outdir= mssdir 
     #imginfosub = mssdf
@@ -110,7 +110,8 @@ mixel = function(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index,outdir,runname
       if(len == 1){newimg = r1} else {eval(parse(text=mergeit))} #only run merge it if there are multiple files to merge
 
       #name the new file
-      newbase = paste(uniyears[i],"_",runname,"_",index,"_composite.bsq", sep="")
+      yearlabel = as.character(as.numeric(uniyears[i])+yearadj)
+      newbase = paste(yearlabel,"_",runname,"_",index,"_composite.bsq", sep="")
       outimgfile = file.path(outdir,newbase)
       outtxtfile = sub("composite.bsq", "composite_img_list.csv", outimgfile)
       theseimgs = data.frame(theseimgs)
@@ -341,7 +342,8 @@ mixel = function(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index,outdir,runname
   for(i in 1:nrow(imginfo)){imginfo$decdate[i] = decyearday(as.numeric(imginfo$year[i]),as.numeric(imginfo$day[i]))}
 
   #figure out the dec year day range that is good
-  uniyears = as.numeric(sort(unique(imginfo$year)))
+  #uniyears = as.numeric(sort(unique(imginfo$year)))
+  uniyears = 1972:as.numeric(format(Sys.Date(),'%Y'))
 
   if(doyears != "all"){uniyears = uniyears[match(doyears,uniyears)]}
 
@@ -376,15 +378,15 @@ mixel = function(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index,outdir,runname
   #create annual composites for all sensors
   if(nrow(mssdf) != 0){
     dir.create(mssdir, recursive=T, showWarnings=F)
-    mixel_composite(mssdir, mssdf, runname=runname,index=index, order=order, useareafile=useareafile, overlap=overlap)
+    mixel_composite(mssdir, mssdf, runname=runname,index=index, order=order, useareafile=useareafile, overlap=overlap, yearadj=yearadj)
   }
   if(nrow(tmetmdf) != 0){
     dir.create(tmdir, recursive=T, showWarnings=F)
-    mixel_composite(tmdir, tmetmdf, runname=runname,index=index, order=order, useareafile=useareafile, overlap=overlap)
+    mixel_composite(tmdir, tmetmdf, runname=runname,index=index, order=order, useareafile=useareafile, overlap=overlap, yearadj=yearadj)
   }
   if(nrow(olidf) != 0){
     dir.create(olidir, recursive=T, showWarnings=F)
-    mixel_composite(olidir, olidf, runname=runname,index=index, order=order, useareafile=useareafile, overlap=overlap)
+    mixel_composite(olidir, olidf, runname=runname,index=index, order=order, useareafile=useareafile, overlap=overlap, yearadj=yearadj)
   }
 
   #deal with the overlapping composites

diff --git a/R/run_landsatlinkr.r b/R/run_landsatlinkr.r
@@ -394,6 +394,19 @@ run_landsatlinkr = function(){
         if(correct == "Exit"){return(cat("Stopping LLR","\n\n"))}
       }
 
+      #figure out how to name the files
+      if((endday-startday) < 0){
+        cat("\n")
+        correct = "No"
+        while(correct == "No"){
+          yearadj = select.list(c("Pre","Post"), title = "Your date range crosses the year divide, would you like to label the annual composite files with the pre- or post- divide year?")
+          cat("You have selected:",yearadj,"\n")
+          correct = select.list(c("Yes","No","Exit"), title = "Is that correct?")
+          if(correct == "Exit"){return(cat("Stopping LLR","\n\n"))}
+        }
+        yearadj = ifelse(yearadj == "Post", 1, 0)
+      }
+
       #overlap methods
       correct = "No"
       while(correct == "No"){
@@ -425,7 +438,7 @@ run_landsatlinkr = function(){
     #################################################################################################################
     #execute the calibrate_and_composite function
 
-    calibrate_and_composite(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index="all",outdir,runname,useareafile,doyears="all",order="none",overlap=overlap, cores=cores, process=calcomprocess, overwrite=overwrite, startday=startday, endday=endday)  #overlap="mean"
+    calibrate_and_composite(msswrs1dir,msswrs2dir,tmwrs2dir,oliwrs2dir,index="all",outdir,runname,useareafile,doyears="all",order="none",overlap=overlap, cores=cores, process=calcomprocess, overwrite=overwrite, startday=startday, endday=endday, yearadj=yearadj)  #overlap="mean"
   }
 
   #if(sum(process %in% 9 > 0)){

diff --git a/man/calibrate_and_composite.Rd b/man/calibrate_and_composite.Rd
diff --git a/man/mixel.Rd b/man/mixel.Rd