require(rshape)

extract_mean_for_roi<-function(covariate_table, mask_file, threshold, float_attribute_id=NULL, can_use_c_code=TRUE, reader_use_mandatory=TRUE)
{
	print("Starting analysis")
	print(Sys.time())
	
	# Read table
	my_data<-read.table(covariate_table, header=TRUE)
		
	# Get the mask
	mask<-getAttributeMask(mask_file, threshold)
	if(is.null(mask)){
		warning("Couldn't load mask file in anova_shape_masked_permute");
		return();
	}
	if(sum(mask)==0){
		warning("No points in the mask exceeded the specified threshold")
		return()
	}
	# Get 4th dimension values
	values<-read_frame_shape_point_masked_attribute_values(my_data, mask, float_attribute_id=float_attribute_id, can_use_c_code=can_use_c_code, reader_use_mandatory=reader_use_mandatory)
	if(is.null(values)){
		warning(paste("failed to load the Shape files specified in '", covariate_table, "'", sep=""));
		return();
	}
	cat("Here are your average ROI values")
	cat("\n")
	for (i in 1:dim(values$atts)[1]){
		cat(mean(values$atts[i,]))
		cat("\n")
	}
}

extract_mean_for_roi("List_of_ucf_files.txt", "ROI.ucf", 0.5)