[Zooimage-commits] r196 - pkg/zooimage/R

[noreply at r-forge.r-project.org]

Author: kevin
Date: 2011-01-20 13:23:19 +0100 (Thu, 20 Jan 2011)
New Revision: 196

Modified:
   pkg/zooimage/R/ZIClass.R
   pkg/zooimage/R/ZITrain.R
Log:
ZIClass: change in "FormVarsSelect" with preselection of varibales to exclude
ZITrain: change in "get.ZITrain" to avoid memory saturation, subset of ZI.sample one by one

Modified: pkg/zooimage/R/ZIClass.R
===================================================================
--- pkg/zooimage/R/ZIClass.R	2010-09-07 10:15:24 UTC (rev 195)
+++ pkg/zooimage/R/ZIClass.R	2011-01-20 12:23:19 UTC (rev 196)
@@ -233,7 +233,7 @@
 #		"Range", "MeanPos", "SDNorm", "CV", "logArea", "logPerim.", "logMajor",
 #		"logMinor", "logFeret"),
 #		multiple = TRUE, title = "Select variables to keep")
-	Notkeep <- select.list(list = mes, preselect = c("Id", "FIT_Cal_Const", "Item", "FIT_Raw_Area", "FIT_Raw_Feret_Max",
+	Notkeep <- select.list(choices = mes, preselect = c("Id", "FIT_Cal_Const", "Item", "FIT_Raw_Area", "FIT_Raw_Feret_Max",
 		"FIT_Raw_Feret_Min", "FIT_Raw_Feret_Mean", "FIT_Raw_Perim", "FIT_Raw_Convex_Perim", "FIT_Feret_Max_Angle",
 		"FIT_Feret_Min_Angle", "FIT_Avg_Red", "FIT_Avg_Green", "FIT_Avg_Blue", "FIT_PPC", "FIT_Ch3_Peak", "FIT_Ch3_TOF",
 		"FIT_Ch4_Peak", "FIT_Ch4_TOF", "FIT_SaveX", "FIT_SaveY", "FIT_PixelW", "FIT_PixelH", "FIT_CaptureX",         

Modified: pkg/zooimage/R/ZITrain.R
===================================================================
--- pkg/zooimage/R/ZITrain.R	2010-09-07 10:15:24 UTC (rev 195)
+++ pkg/zooimage/R/ZITrain.R	2011-01-20 12:23:19 UTC (rev 196)
@@ -105,14 +105,14 @@
 	checkDirExists(dir)
 
 	# Make sure we have .RData files in this dir (otherwise it is perhaps not a
-    # training set root dir!
-    Dats <- list.files(dir, pattern = "_dat1[.]RData$", full.names = TRUE)
+	# training set root dir!
+	Dats <- list.files(dir, pattern = "_dat1[.]RData$", full.names = TRUE)
 	if (length(Dats) == 0)
 		stop("does not appear to be a ", getTemp("ZIname"),
 			" training set root dir!")
 
 	# list the jpg files (recursively) in the dir
-    res <- list.files.ext(dir, extension = "jpg", recursive = TRUE)
+	res <- list.files.ext(dir, extension = "jpg", recursive = TRUE)
 
 	# Check the result...
 	if (length(res) < 1)
@@ -136,7 +136,7 @@
 	# Create a directory (a data frame with: Id, Class)
 	df <- data.frame(Id = Id, Class = Class)
 	df$Id <- as.character(df$Id)
-    nitems <- nrow(df)
+	nitems <- nrow(df)
 
 	# Read in all the .RData files from the root directory and merge them
     ### TODO: also collect metadata and merge them => make a merge function for
@@ -148,20 +148,37 @@
 	load(Dats[1])
 	Dat <- ZI.sample
 	Classes <- class(Dat)
+	
+	# Modif Kev to free memory
+	Dat <- cbind(Id = make.Id(Dat), Dat)
+	Dat <- merge(Dat, df, by = "Id")
+
 	if (length(Dats) > 1) {
 		for (i in 2:length(Dats)) {
 			load(Dats[i])
+			ZI.sample <- cbind(Id = make.Id(ZI.sample), ZI.sample)
+			ZI.sample <- merge(ZI.sample, df, by = "Id")
 			Dat <- rbind(Dat, ZI.sample)
 		}
 	}
+	
+#	if (length(Dats) > 1) {
+#		for (i in 2:length(Dats)) {
+#			load(Dats[i])
+#			Dat <- rbind(Dat, ZI.sample)
+#		}
+#	}
+
 	rownames(Dat) <- 1:nrow(Dat)
 
 	# Create the Id column
-	Dat <- cbind(Id = make.Id(Dat), Dat)
+# Done in the loop!
+#	Dat <- cbind(Id = make.Id(Dat), Dat)
 
 	# Merge Dat & df by "Id"
-	df <- merge(Dat, df, by = "Id")
-
+#	df <- merge(Dat, df, by = "Id")
+	# rename Dat in df
+	df <- Dat
 	# Issue an error if there is no remaing row in the data frame
 	if (nrow(df) == 0)
 		stop("No valid item found (both with a vignette and with valid measurement data!")