Merge pull request #24 from scizmeli/dev

Baris please pull Tasks/Defects 8744 8854 and 8761

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: geoSpectral
 Type: Package
-Title: Classes and methods for spectral (optical) data
+Title: Classes and methods for working with spectral (electromagnetic) data in R.
 Version: 0.11
 Date: 2012-07-02
 Depends:

R/Spectra-Class.R

@@ -1,33 +1,26 @@
-# TODO: Add comment
-# 
-# Author: acizmeli
-###############################################################################
 #########################################################################
 # Class : Spectra
 #########################################################################
 #' Create a spectra class definition
 #' @description
-#' Create a spectra class definition, specifying the representation (the slots) and/or the classes contained in this one (the superclasses),
-#' plus other optional details. As a side effect, the class definition is stored in the specified environment
-#'
-#' @usage 
-#' setClass(class, contains,pepresentation,prototype)
-#' 
-#' 
-#'
-#' 
-#' @param  contains STIDF 
-#' @param class  character string name for the class.
-#' @param  pepresentation avoided
-#' @param  prototype n object providing the default data for the slots in this class
-#' 
-#' 
-#' 
-#' 
-#' 
-#' 
-#' 
-#' 
+#' Spectra class is the main class provided by the package geoSpectRal. It allows storage
+#' of spectral or non-spectra data with space and time attributes.
+#' @slot ShortName character, A short name for the parameter described in the spectra object. 
+#' @slot LongName character, A long name for the parameter described in the spectra object. 
+#' @slot Spectra matrix, n by m matrix, describing n rows of spectral data
+#'  (or time) in m channels (columns).
+#' @slot data data.frame n by t data frame, describind n rows of ancillary data
+#' of t variables. This slot is inherited from STIDF class. 
+#' @slot Wavelengths numeric vector, length of m. Wavelength data. 
+#' @slot WavelengthsUnit character,  Units of the @Wavelength slot
+#' @slot header SpcHeader, Header object. See SpcHeader-class.
+#' @slot Units character, Units of spectral data.
+#' @slot UnitsAnc character, Units of each column of the @data slot holding ancillary data.
+#' @slot ShortNameAnc character, A short name for each column of the @data slot holding ancillary data.
+#' @slot LongNameAnc character, A long name for each column of the @data slot holding ancillary data.
+#' @slot InvalidIdx logical, length of m. Row index for measurements marked by the user as invalid.
+#' @slot SelectedIdx logical, length of m. Row index for measurements marked by the user as selected.
+#' @slot ClassVersion numeric, Version of the class.
 setClass("Spectra", contains="STIDF", 
 		representation=representation(
 				ShortName="character",

R/Spectra-Methods.R

@@ -1993,54 +1993,60 @@ spc.header.infos = function(header){
 #' 
 #'@details
 #' \code{spc.export.xlsx()} calls functions from package \code{xlsx} to write the contents of 
-#' a \code{Spectra} object into an Excel file.
+#' a \code{Spectra} object into an Excel file. Make sure \code{xlsx} is installed.
 #' 
 #' @return None. Simply creates an Excel file on disk.
 #'
 #' @examples
-#' sp=spc.example_spectra()
-#' if("xlsx" %in% installed.packages())
-#'    spc.export.xlsx(sp,"test.xlsx")
+#' \dontrun{
+#'   sp=spc.example_spectra()
+#'   if("xlsx" %in% installed.packages())
+#'      spc.export.xlsx(sp,"test.xlsx")
+#' }
 setGeneric(name="spc.export.xlsx",
            def=function(input,filename,sheetName,writeheader=TRUE,append=F,sep=";",...) {standardGeneric("spc.export.xlsx")})
 setMethod("spc.export.xlsx", signature="Spectra", definition=function(input,filename,sheetName,writeheader,append,sep,...){
-  if(missing(sheetName))
-    sheetName = input@ShortName
-  data = as(input,"data.frame")
-  data$TIME = as.character(data$TIME,usetz=TRUE)
-  data$ENDTIME = as.character(data$ENDTIME,usetz=TRUE)
-  data = cbind(data.frame(idx=1:nrow(data)),data)
-
-  slotInfos = .spc.slot.infos(input,sep)
-  if(!append){
-    #Create an empty excel workbook and start writing into it
-    wb <- xlsx::createWorkbook()
-  }else{
-    #Create an empty excel workbook and start writing into it
-    wb <- xlsx::loadWorkbook(file=filename)
-  }
-  sheet <- xlsx::createSheet(wb, sheetName=sheetName)
-  if(writeheader){
-    for(I in 1:length(input@header)){					
-      if(length(input@header[[I]])==1)
-        myH=cbind("Spectra|header",names(input@header)[I],input@header[[I]])
-      else		
-        myH = cbind("Spectra|header",names(input@header)[I],t(input@header[[I]]))
-      xlsx::addDataFrame(myH, sheet,row.names=F,col.names=F,,startRow=I,startColumn=1)
+  if (!requireNamespace("xls", quietly = TRUE)) {
+    print("xlsx needed for this function to work. Please install it.")
+  } else {
+    if(missing(sheetName))
+      sheetName = input@ShortName
+    data = as(input,"data.frame")
+    data$TIME = as.character(data$TIME,usetz=TRUE)
+    data$ENDTIME = as.character(data$ENDTIME,usetz=TRUE)
+    data = cbind(data.frame(idx=1:nrow(data)),data)
+
+    slotInfos = .spc.slot.infos(input,sep)
+    if(!append){
+      #Create an empty excel workbook and start writing into it
+      wb <- xlsx::createWorkbook()
+    }else{
+      #Create an empty excel workbook and start writing into it
+      wb <- xlsx::loadWorkbook(file=filename)
     }
+    sheet <- xlsx::createSheet(wb, sheetName=sheetName)
+    if(writeheader){
+      for(I in 1:length(input@header)){					
+        if(length(input@header[[I]])==1)
+          myH=cbind("Spectra|header",names(input@header)[I],input@header[[I]])
+        else		
+          myH = cbind("Spectra|header",names(input@header)[I],t(input@header[[I]]))
+        xlsx::addDataFrame(myH, sheet,row.names=F,col.names=F,,startRow=I,startColumn=1)
+      }
+    }
+    written = length(input@header)
+    for(I in 1:length(slotInfos)){
+      if(length(slotInfos[[I]])==1)
+        mysl=cbind(names(slotInfos)[I],slotInfos[[I]])
+      else
+        mysl = cbind(names(slotInfos)[I],t(slotInfos[[I]]))
+      xlsx::addDataFrame(mysl,sheet,row.names=F,col.names=F,startRow=written+1,startColumn=1)
+      written = written+1
+    }
+    xlsx::addDataFrame(data, sheet,row.names=F,startRow=written+1,startColumn=1)
+    xlsx::saveWorkbook(wb, filename)
+    print(paste("Wrote sheet", sheetName, "to", filename))
   }
-  written = length(input@header)
-  for(I in 1:length(slotInfos)){
-    if(length(slotInfos[[I]])==1)
-      mysl=cbind(names(slotInfos)[I],slotInfos[[I]])
-    else
-      mysl = cbind(names(slotInfos)[I],t(slotInfos[[I]]))
-    xlsx::addDataFrame(mysl,sheet,row.names=F,col.names=F,startRow=written+1,startColumn=1)
-    written = written+1
-  }
-  xlsx::addDataFrame(data, sheet,row.names=F,startRow=written+1,startColumn=1)
-  xlsx::saveWorkbook(wb, filename)
-  print(paste("Wrote sheet", sheetName, "to", filename))
 })
 
 #########################################################################

R/geoSpectral.R

@@ -1,4 +1,4 @@
-#' @title Manipulation of spectral (electromagnetic) data
+#' @title Classes and methods for working with spectral (electromagnetic) data in R.
 #'
 #' @description 
 #' \pkg{geoSpectral} is an R package providing a new data type for R that stores