Updated documentation. Created new convolve.spectra() function. Currently only works with AVIRIS data. A work in progress and needs updates to generalize the function for multiple sensors.

Author: Shawn P. Serbin

DESCRIPTION

@@ -23,10 +23,3 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-Collate:
-    'import.asd.R'
-    'read.asd.R'
-    'spec.utils.R'
-    'average.spec.R'
-    'jump.correction.R'
-    'average.spec.se.R'

FieldSpectra-manual.pdf

@@ -1,6 +1,7 @@
-export(average.spec.se)
 export(average.spec)
+export(average.spec.se)
 export(concat.spectra)
+export(convolve.spectra)
 export(extract.metadata)
 export(import.asd)
 export(jump.correction)

NAMESPACE

@@ -30,7 +30,7 @@
 ##'
 ##'@examples
 ##' # Set input file
-##' file.dir <- system.file("extdata/PM01_TIAM_B_LC_REFL00005.asd",package="FieldSpec")
+##' file.dir <- system.file("extdata/PM01_TIAM_B_LC_REFL00005.asd",package="FieldSpectra")
 ##' spec <- read.asd(file.dir,out.dir='~',start.wave=350,end.wave=2500,step.size=1)
 ##' 
 ##' # Get info from file header

R/read.asd.R

@@ -75,11 +75,11 @@ settings <- function(input.file=NULL){
 ##' 
 ##' @examples
 ##' # ASD
-##' file <- system.file("extdata/PM01_TIAM_B_LC_REFL00005.asd",package="FieldSpec")
+##' file <- system.file("extdata/PM01_TIAM_B_LC_REFL00005.asd",package="FieldSpectra")
 ##' output <- extract.metadata(file,instrument="ASD")
 ##' 
 ##' # Spectral Evolution
-##' file <- system.file("extdata/cvars_grape_leaf1_lc_rg_01236.sed",package="FieldSpec")
+##' file <- system.file("extdata/cvars_grape_leaf1_lc_rg_01236.sed",package="FieldSpectra")
 ##' output <- extract.metadata(file,instrument="SE")
 ##' 
 ##' @author Shawn P. Serbin
@@ -962,15 +962,85 @@ smooth.spectra <- function(file.dir=NULL,input.file=NULL,out.dir=NULL,out.filena
 #--------------------------------------------------------------------------------------------------#
 ##' 
 ##' @name convolve.spectra
-##' @title Convolve field spectral observations to airborne/satellite spectral bands/channels
+##' @title Convolve field spectral observations to airborne/satellite spectral bands/channels.
 ##' 
-##' @param
+##' @param field.spectra Input field spectra. If a single spectra then the format can be either
+##' column or row major with the wavelengths either a column of data or the column headers.  If
+##' multiple (i.e. a matrix of data) the input should be in row major format with the column headers
+##' as wavelength numbers.  See examples below.
+##' @param start.wave Starting wavelength of field spectra
+##' @param end.wave ending wavelength of field spectra
+##' @param sensor The sensor (e.g. "AVIRIS", "Landsat 5", "Landsat 7", "MODIS").  Current options
+##' are: "AVIRIS"  More to come in the future
+##' @param year [Optional] E.g. year=2011.  If the AVIRIS sensor is selected this allows the user
+##' to select a specific spectral calibration based on the year of data aquisition.
+##' Defaults to 2011.
+##' @param spc [Optional] Option to use custom spectral calibration information.  Format:
+##' band number, center wavelength, FWHM.  NOT YET IMPLEMENTED 
+##' @param output.dir [Optional] Directory to output the convolved spectral data.  If not set
+##' the results are only pasesd back to the working environment
+##' 
+##' @return output.spectra Returns a matrix of convolved spectra
+##' 
+##' @export
 ##' 
 ##' @author Shawn P. Serbin
 ##'
-convolve.spectra <- function(spectra){ 
+convolve.spectra <- function(field.spectra=NULL,start.wave=NULL,end.wave=NULL,sensor=NULL,year=NULL,
+                             spc=NULL){ 
+  
+  # Determine sensor type
+  if (sensor=="AVIRIS"){
+    if (is.null(year)) {
+      sensor.file <- system.file("extdata/AVIRIS_2011_SPC_Info.csv",package="FieldSpectra")
+      sensor.spc <- read.table(sensor.file,header=F, col.names = c('Band_Number','Wavelength','FWHM'), 
+                               sep=",")
+    } else {
+      print("Not Implemented Yet")
+    } # End AVIRIS if/else
+    
+  } else {
+    print(paste0(sensor,":"," Not Implemented Yet"))
+  } ## End main if/else
+  
+  ## Convert field spectra to matrix
+  field.spectra <- as.matrix(field.spectra)
+  # Temp
+  #field.spectra <- field.spectra[1,]
+  
+  ## 
+  wvlArr <- as.array(sensor.spc[,2])
+  fwhArr <- as.array(sensor.spc[,3])
+  fs_wvArr <- as.array(seq(start.wave,end.wave,1))
+  keep <- which(round(wvlArr) %in% fs_wvArr,arr.ind=T)
+  wvlArr <- wvlArr[keep]
+  fwhArr <- fwhArr[keep]
+  convArr <- as.vector(rep(NA,1,length(fwhArr)))
+  output.spectra <- array(data=NA,dim=c(dim(field.spectra)[1],length(fwhArr)))
 
+  ## Generic convolve function
+  for (i in 1:dim(field.spectra)[1]) {
+    for (band in 1:length(wvlArr)) {
+      #print(band)
+      ### Create convolution kernel (from http://en.wikipedia.org/wiki/Gaussian_function)
+      convKern <- exp(-(fs_wvArr-wvlArr[band])^2/(2*(fwhArr[band]^2)))
+      ### Normalize the kernel
+      convKern <- convKern/sum(convKern)
+      ### Generate output band
+      convArr[band] <- sum(convKern*field.spectra[i,])
+    }
+    output.spectra[i,] <- convArr
+  } # End main for loop
+  output <- list(Wavelengths=wvlArr,Spectra=output.spectra)
+  invisible(output) # output convolved spectra
 }
+
+# for debugging
+#plot(wvlArr,convArr,type="l")
+#lines(seq(350,2500,1),unlist(field.spectra),type="l")
+
+#plot(wvlArr,output.spectra[15,],type="l")
+#lines(seq(350,2500,1),unlist(field.spectra[15,]),type="l")
 #==================================================================================================#
 
 

R/spec.utils.R

@@ -1 +1 @@
-Band_Number,Wavelength,FWHM1,365.93,9.852112,375.594,9.796983,385.263,9.74414,394.935,9.693495,404.613,9.645146,414.295,9.599057,423.981,9.555228,433.671,9.513649,443.366,9.4743310,453.065,9.4372811,462.769,9.4024912,472.477,9.3699613,482.19,9.3396814,491.907,9.3116715,501.628,9.2859216,511.353,9.2624317,521.084,9.241218,530.818,9.2222219,540.557,9.2055120,550.3,9.1910621,560.048,9.1788722,569.8,9.1689423,579.556,9.1612624,589.317,9.1558525,599.082,9.152726,608.852,9.1518127,618.625,9.1531828,628.404,9.156829,638.187,9.1626930,647.974,9.1708431,657.765,9.1812532,667.561,9.1939233,655.792,9.9084734,665.599,9.8487135,675.401,9.7987136,685.198,9.7584837,694.989,9.7280238,704.776,9.7073239,714.557,9.696440,724.333,9.6952341,734.103,9.7038442,743.869,9.7222143,753.629,9.7503544,763.384,9.7882545,773.133,9.8359346,782.878,9.8933647,792.617,9.9605748,802.352,10.037549,812.081,10.124350,821.804,10.220851,831.523,10.327152,841.236,10.443153,850.944,10.568954,860.647,10.704555,870.345,10.849856,880.037,11.004957,889.724,11.169858,899.407,11.344459,909.083,11.528860,918.755,11.72361,928.421,11.92762,938.083,10.781563,947.739,9.761864,957.39,9.7600665,967.035,9.7593266,976.675,9.7595967,986.311,9.7608568,995.941,9.7631169,1005.57,9.7663770,1015.18,9.7706371,1024.8,9.775972,1034.41,9.7821673,1044.01,9.7894274,1053.61,9.7976975,1063.2,9.8069576,1072.79,9.8172277,1082.38,9.8284978,1091.95,9.8407579,1101.53,9.8540280,1111.09,9.8682981,1120.66,9.8835682,1130.21,9.8998383,1139.77,9.9170984,1149.31,9.9353685,1158.85,9.9546386,1168.39,9.9749187,1177.92,9.9961888,1187.45,10.018489,1196.97,10.041790,1206.48,10.06691,1215.99,10.091392,1225.5,10.117593,1235,10.144894,1244.49,10.173195,1253.98,10.202496,1263.46,10.232697,1253.37,10.838398,1263.35,10.832799,1273.32,10.8272100,1283.29,10.8219101,1293.26,10.8167102,1303.23,10.8117103,1313.21,10.8067104,1323.18,10.802105,1333.15,10.7973106,1343.12,10.7928107,1353.09,10.7885108,1363.06,10.7843109,1373.03,10.7802110,1383,10.7762111,1392.97,10.7724112,1402.94,10.7687113,1412.91,10.7652114,1422.88,10.7618115,1432.84,10.7585116,1442.81,10.7554117,1452.78,10.7524118,1462.75,10.7496119,1472.72,10.7469120,1482.69,10.7443121,1492.65,10.7419122,1502.62,10.7396123,1512.59,10.7374124,1522.55,10.7354125,1532.52,10.7335126,1542.48,10.7317127,1552.45,10.7301128,1562.42,10.7287129,1572.38,10.7273130,1582.35,10.7261131,1592.31,10.7251132,1602.28,10.7241133,1612.24,10.7233134,1622.2,10.7227135,1632.17,10.7222136,1642.13,10.7218137,1652.09,10.7216138,1662.06,10.7215139,1672.02,10.7215140,1681.98,10.7217141,1691.94,10.722142,1701.91,10.7225143,1711.87,10.7231144,1721.83,10.7238145,1731.79,10.7247146,1741.75,10.7256147,1751.71,10.7268148,1761.68,10.7281149,1771.64,10.7295150,1781.6,10.731151,1791.56,10.7327152,1801.52,10.7346153,1811.47,10.7365154,1821.43,10.7386155,1831.39,10.7409156,1841.35,10.7432157,1851.31,10.7457158,1861.27,10.7484159,1871.23,10.7512160,1872.38,10.7541161,1866.86,11.1666162,1876.93,11.1579163,1886.98,11.1489164,1897.04,11.1396165,1907.1,11.1299166,1917.15,11.1199167,1927.2,11.1096168,1937.25,11.099169,1947.29,11.0881170,1957.33,11.0769171,1967.38,11.0653172,1977.41,11.0534173,1987.45,11.0413174,1997.48,11.0288175,2007.52,11.0159176,2017.55,11.0028177,2027.57,10.9893178,2037.6,10.9755179,2047.62,10.9615180,2057.64,10.9471181,2067.66,10.9323182,2077.67,10.9173183,2087.69,10.9019184,2097.7,10.8863185,2107.7,10.8703186,2117.71,10.854187,2127.71,10.8373188,2137.72,10.8204189,2147.72,10.8031190,2157.71,10.7856191,2167.71,10.7677192,2177.7,10.7494193,2187.69,10.7309194,2197.68,10.7121195,2207.66,10.6929196,2217.65,10.6734197,2227.63,10.6537198,2237.6,10.6335199,2247.58,10.6131200,2257.55,10.5924201,2267.53,10.5713202,2277.5,10.5499203,2287.46,10.5282204,2297.43,10.5062205,2307.39,10.4839206,2317.35,10.4612207,2327.31,10.4383208,2337.26,10.415209,2347.22,10.3914210,2357.17,10.3675211,2367.11,10.3433212,2377.06,10.3187213,2387,10.2938214,2396.95,10.2687215,2406.89,10.2432216,2416.82,10.2174217,2426.76,10.1912218,2436.69,10.1648219,2446.62,10.138220,2456.55,10.1109221,2466.47,10.0835222,2476.4,10.0558223,2486.32,10.0278224,2496.24,9.99943
+1,365.93,9.852112,375.594,9.796983,385.263,9.74414,394.935,9.693495,404.613,9.645146,414.295,9.599057,423.981,9.555228,433.671,9.513649,443.366,9.4743310,453.065,9.4372811,462.769,9.4024912,472.477,9.3699613,482.19,9.3396814,491.907,9.3116715,501.628,9.2859216,511.353,9.2624317,521.084,9.241218,530.818,9.2222219,540.557,9.2055120,550.3,9.1910621,560.048,9.1788722,569.8,9.1689423,579.556,9.1612624,589.317,9.1558525,599.082,9.152726,608.852,9.1518127,618.625,9.1531828,628.404,9.156829,638.187,9.1626930,647.974,9.1708431,657.765,9.1812532,667.561,9.1939233,675.401,9.7987134,685.198,9.7584835,694.989,9.7280236,704.776,9.7073237,714.557,9.696438,724.333,9.6952339,734.103,9.7038440,743.869,9.7222141,753.629,9.7503542,763.384,9.7882543,773.133,9.8359344,782.878,9.8933645,792.617,9.9605746,802.352,10.037547,812.081,10.124348,821.804,10.220849,831.523,10.327150,841.236,10.443151,850.944,10.568952,860.647,10.704553,870.345,10.849854,880.037,11.004955,889.724,11.169856,899.407,11.344457,909.083,11.528858,918.755,11.72359,928.421,11.92760,938.083,10.781561,947.739,9.761862,957.39,9.7600663,967.035,9.7593264,976.675,9.7595965,986.311,9.7608566,995.941,9.7631167,1005.57,9.7663768,1015.18,9.7706369,1024.8,9.775970,1034.41,9.7821671,1044.01,9.7894272,1053.61,9.7976973,1063.2,9.8069574,1072.79,9.8172275,1082.38,9.8284976,1091.95,9.8407577,1101.53,9.8540278,1111.09,9.8682979,1120.66,9.8835680,1130.21,9.8998381,1139.77,9.9170982,1149.31,9.9353683,1158.85,9.9546384,1168.39,9.9749185,1177.92,9.9961886,1187.45,10.018487,1196.97,10.041788,1206.48,10.06689,1215.99,10.091390,1225.5,10.117591,1235,10.144892,1244.49,10.173193,1253.98,10.202494,1263.46,10.232695,1273.32,10.827296,1283.29,10.821997,1293.26,10.816798,1303.23,10.811799,1313.21,10.8067100,1323.18,10.802101,1333.15,10.7973102,1343.12,10.7928103,1353.09,10.7885104,1363.06,10.7843105,1373.03,10.7802106,1383,10.7762107,1392.97,10.7724108,1402.94,10.7687109,1412.91,10.7652110,1422.88,10.7618111,1432.84,10.7585112,1442.81,10.7554113,1452.78,10.7524114,1462.75,10.7496115,1472.72,10.7469116,1482.69,10.7443117,1492.65,10.7419118,1502.62,10.7396119,1512.59,10.7374120,1522.55,10.7354121,1532.52,10.7335122,1542.48,10.7317123,1552.45,10.7301124,1562.42,10.7287125,1572.38,10.7273126,1582.35,10.7261127,1592.31,10.7251128,1602.28,10.7241129,1612.24,10.7233130,1622.2,10.7227131,1632.17,10.7222132,1642.13,10.7218133,1652.09,10.7216134,1662.06,10.7215135,1672.02,10.7215136,1681.98,10.7217137,1691.94,10.722138,1701.91,10.7225139,1711.87,10.7231140,1721.83,10.7238141,1731.79,10.7247142,1741.75,10.7256143,1751.71,10.7268144,1761.68,10.7281145,1771.64,10.7295146,1781.6,10.731147,1791.56,10.7327148,1801.52,10.7346149,1811.47,10.7365150,1821.43,10.7386151,1831.39,10.7409152,1841.35,10.7432153,1851.31,10.7457154,1861.27,10.7484155,1871.23,10.7512156,1876.93,11.1579157,1886.98,11.1489158,1897.04,11.1396159,1907.1,11.1299160,1917.15,11.1199161,1927.2,11.1096162,1937.25,11.099163,1947.29,11.0881164,1957.33,11.0769165,1967.38,11.0653166,1977.41,11.0534167,1987.45,11.0413168,1997.48,11.0288169,2007.52,11.0159170,2017.55,11.0028171,2027.57,10.9893172,2037.6,10.9755173,2047.62,10.9615174,2057.64,10.9471175,2067.66,10.9323176,2077.67,10.9173177,2087.69,10.9019178,2097.7,10.8863179,2107.7,10.8703180,2117.71,10.854181,2127.71,10.8373182,2137.72,10.8204183,2147.72,10.8031184,2157.71,10.7856185,2167.71,10.7677186,2177.7,10.7494187,2187.69,10.7309188,2197.68,10.7121189,2207.66,10.6929190,2217.65,10.6734191,2227.63,10.6537192,2237.6,10.6335193,2247.58,10.6131194,2257.55,10.5924195,2267.53,10.5713196,2277.5,10.5499197,2287.46,10.5282198,2297.43,10.5062199,2307.39,10.4839200,2317.35,10.4612201,2327.31,10.4383202,2337.26,10.415203,2347.22,10.3914204,2357.17,10.3675205,2367.11,10.3433206,2377.06,10.3187207,2387,10.2938208,2396.95,10.2687209,2406.89,10.2432210,2416.82,10.2174211,2426.76,10.1912212,2436.69,10.1648213,2446.62,10.138214,2456.55,10.1109215,2466.47,10.0835216,2476.4,10.0558217,2486.32,10.0278218,2496.24,9.99943

inst/extdata/AVIRIS_2011_SPC_Info.csv

@@ -1,4 +1,4 @@
-list.of.packages <- c('XML','Hmisc','testthat','signal') 
+list.of.packages <- c('XML','Hmisc','testthat','signal','Rcpp') 
 
 new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
 if(length(new.packages)) {

inst/install.dependencies.R

@@ -2,11 +2,10 @@
 \alias{average.spec}
 \title{average replicate spectra within a directory of spectra files}
 \usage{
-  average.spec(file.dir = NULL, out.dir = NULL,
-    start.wave = NULL, end.wave = NULL, step.size = NULL,
-    bias.threshold = NULL, suffix.length = NULL,
-    output.file.ext = NULL, metadata.file = NULL,
-    image = FALSE, settings.file = NULL)
+average.spec(file.dir = NULL, out.dir = NULL, start.wave = NULL,
+  end.wave = NULL, step.size = NULL, bias.threshold = NULL,
+  suffix.length = NULL, output.file.ext = NULL, metadata.file = NULL,
+  image = FALSE, settings.file = NULL)
 }
 \arguments{
   \item{file.dir}{Directory of spectra files to process}
@@ -59,8 +58,8 @@
   function call.}
 }
 \description{
-  Function to average replicate spectra within a directory
-  of spectra files
+Function to average replicate spectra within a directory of
+spectra files
 }
 \examples{
 \dontrun{
@@ -70,6 +69,6 @@ suffix.length=5,output.file.ext=".csv",spec.dataframe = TRUE,)
 }
 }
 \author{
-  Shawn P. Serbin
+Shawn P. Serbin
 }
 

man/average.spec.Rd

@@ -2,11 +2,10 @@
 \alias{average.spec.se}
 \title{average replicate spectra within a directory of spectra files}
 \usage{
-  average.spec.se(file.dir = NULL, out.dir = NULL,
-    spec.type = NULL, spec.file.ext = NULL,
-    start.wave = NULL, end.wave = NULL, step.size = NULL,
-    bias.threshold = NULL, suffix.length = NULL,
-    output.file.ext = NULL, settings.file = NULL)
+average.spec.se(file.dir = NULL, out.dir = NULL, spec.type = NULL,
+  spec.file.ext = NULL, start.wave = NULL, end.wave = NULL,
+  step.size = NULL, bias.threshold = NULL, suffix.length = NULL,
+  output.file.ext = NULL, settings.file = NULL)
 }
 \arguments{
   \item{file.dir}{directory of spectra files to process}
@@ -52,10 +51,10 @@
   function call.}
 }
 \description{
-  Function to average replicate spectra within a directory
-  of spectra files
+Function to average replicate spectra within a directory of
+spectra files
 }
 \author{
-  Shawn P. Serbin
+Shawn P. Serbin
 }
 

man/average.spec.se.Rd

@@ -3,10 +3,9 @@
 \title{Concatenate a directory of spectra files into a single .csv file. Works on a single
 directory or a series of directories}
 \usage{
-  concat.spectra(file.dir = NULL, out.dir = NULL,
-    out.filename = NULL, in.file.ext = ".csv",
-    out.file.ext = ".csv", transpose = FALSE,
-    spec.dataframe = FALSE)
+concat.spectra(file.dir = NULL, out.dir = NULL, out.filename = NULL,
+  in.file.ext = ".csv", out.file.ext = ".csv", transpose = FALSE,
+  spec.dataframe = FALSE)
 }
 \arguments{
   \item{file.dir}{directory of spectra files to process.
@@ -35,9 +34,7 @@ directory or a series of directories}
   containing the concatenated spectral data.  TRUE/FALSE}
 }
 \description{
-  Concatenate a directory of spectra files into a single
-  .csv file. Works on a single directory or a series of
-  directories
+
 }
 \examples{
 \dontrun{
@@ -47,6 +44,6 @@ out.file.ext=".csv",transpose=FALSE,spec.dataframe=FALSE)
 }
 }
 \author{
-  Shawn P. Serbin
+Shawn P. Serbin
 }