Getting conversions from RGB to work directly on images

R/rgb.R

@@ -54,7 +54,7 @@ as.character.rgbArray <- function (x, ...)
 #' @export
 extractChannels <- function (array, channels = c("red","green","blue","alpha"), raw = FALSE)
 {
-    if (!inherits(array, "rgbArray"))
+    if (!inherits(array,"niftiImage") && !inherits(array,"rgbArray"))
         array <- rgbArray(array)
 
     channels <- match.arg(channels, several.ok=TRUE)
@@ -63,6 +63,6 @@ extractChannels <- function (array, channels = c("red","green","blue","alpha"),
     result <- .Call("unpackRgb", array, channelNumbers, PACKAGE="RNifti")
     if (!raw)
         storage.mode(result) <- "integer"
-    dimnames(result) <- list(NULL, channels)
+    dimnames(result) <- c(rep(list(NULL),ndim(array)), list(channels))
     return (result)
 }

src/main.cpp

@@ -88,18 +88,16 @@ END_RCPP
 RcppExport SEXP rgbToStrings (SEXP _object)
 {
 BEGIN_RCPP
-    IntegerVector array(_object);
-    const int channels = array.attr("channels");
-    const size_t len = Rf_length(array);
-
-    CharacterVector result(len);
-    for (size_t i=0; i<len; i++)
+    const NiftiImage image(_object, true, true);
+    const NiftiImageData data = image.data();
+    CharacterVector result(image.nVoxels());
+    for (size_t i=0; i<image.nVoxels(); i++)
     {
         rgba32_t rgba;
-        rgba.value.packed = array[i];
+        rgba.value.packed = int(data[i]);
         std::ostringstream value;
         value << "#" << std::hex << std::uppercase;
-        for (int j=0; j<channels; j++)
+        for (int j=0; j<image.nChannels(); j++)
             value << std::setw(2) << std::setfill('0') << int(rgba.value.bytes[j]);
         result[i] = value.str();
     }
@@ -110,21 +108,22 @@ END_RCPP
 RcppExport SEXP unpackRgb (SEXP _object, SEXP _channels)
 {
 BEGIN_RCPP
-    IntegerVector array(_object);
+    const NiftiImage image(_object, true, true);
+    const NiftiImageData data = image.data();
     const int_vector channels = as<int_vector>(_channels);
-
-    int_vector dim = array.attr("dim");
+    int_vector dim = image.dim();
     dim.push_back(channels.size());
-    const size_t len = Rf_length(array);
+
+    const size_t len = image.nVoxels();
     RawVector result(len * channels.size());
     rgba32_t rgba;
     for (size_t i=0; i<len; i++)
     {
-        rgba.value.packed = array[i];
-        for (int_vector::const_iterator it=channels.begin(); it<channels.end(); ++it)
+        rgba.value.packed = int(data[i]);
+        for (int j=0; j<channels.size(); j++)
         {
-            const int channel = (*it) - 1;
-            result[i + len * channel] = rgba.value.bytes[channel];
+            const int channel = channels[j] - 1;
+            result[i + len * j] = int(rgba.value.bytes[channel]);
         }
     }
     result.attr("dim") = dim;

tests/testthat/test-08-composite.R

@@ -32,13 +32,15 @@ test_that("RGB datatypes are handled properly", {
     k <- stats::kmeans(as.vector(image), 3L)
     data <- rgbArray(k$cluster==1, k$cluster==2, k$cluster==3, dim=dim(image))
     rgbImage <- updateNifti(data, image)
-    refValue <- rgbArray(diag(3))[k$cluster[40 + 39*96 + 29*9216]]
+    cluster <- k$cluster[40 + 39*96 + 29*9216]
+    refValue <- rgbArray(diag(3))[cluster]
 
     expect_s3_class(data, "rgbArray")
     expect_equal(rgbImage[40,40,30], refValue)
     expect_equal(rgbImage$datatype, 128L)
     expect_equal(rgbImage$bitpix, 24L)
     expect_equivalent(unclass(data), unclass(as.array(rgbImage)))
+    expect_equivalent(extractChannels(rgbImage,c("red","green","blue")[cluster])[40,40,30,1], 255L)
 
     writeNifti(rgbImage, tempPath)
     header <- niftiHeader(tempPath)