Merge pull request #8 from muschellij2/master

Fixing NAs

CRAN-RELEASE

@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2020-01-24.
-Once it is accepted, delete this file and tag the release (commit 2701b70d47).
+This package was submitted to CRAN on 2020-05-28.
+Once it is accepted, delete this file and tag the release (commit 3420c8ea90).

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: oro.nifti
-Version: 0.10.2
+Version: 0.10.3
 Title: Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output
 Authors@R: 
     c(person(given = "Brandon",
@@ -165,6 +165,6 @@ Collate:
     'img_length.R'
     'zzz.R'
     'zzz_niftiImage.R'
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
 Encoding: UTF-8
 

NEWS.md

@@ -1,3 +1,7 @@
+# oro.nifti 0.10.3
+
+* Fixing when there are any `NA` values.
+
 # oro.nifti 0.10.1
 
 * Added an `origin` accessor for `nifti` objects.

R/writeS4.R

@@ -155,9 +155,14 @@ setMethod("writeNIfTI", signature(nim="array"),
 
 .writeNIfTI <- function(nim, filename, onefile=TRUE, gzipped=TRUE,
                         verbose=FALSE, warn=-1, compression = 6) {
+
   ## Warnings?
   oldwarn <- getOption("warn")
   options(warn=warn)
+  any_na = anyNA(nim@.Data)
+  if (any_na) {
+    warning("NAs may be turned to NaNs")
+  }  
   #### added so that range of the data will equal cal.min/cal.max
   nim <- calibrateImage(nim)
   ##### Added so that bad dimensions are dropped
@@ -198,6 +203,18 @@ setMethod("writeNIfTI", signature(nim="array"),
       cat("  vox_offset =", nim@"vox_offset", fill=TRUE)
     }
   }
+  ## reorient?
+  if (nim@"reoriented") {
+    data <- as.vector(inverseReorient(nim))
+  } else {
+    data <- as.vector(nim@.Data)
+  }
+  if (any_na) {
+    warning("Need to change bitpix and datatype to FLOAT32 due to NAs")
+    nim@"datatype" = max(16L, nim@datatype)
+    nim@bitpix = max(64L, nim@bitpix)
+  }
+
   ##
   writeBin(as.integer(nim@"sizeof_hdr"), fid, size=4)
   writeChar(nim@"data_type", fid, nchars=10, eos=NULL)
@@ -270,16 +287,12 @@ setMethod("writeNIfTI", signature(nim="array"),
       stop("@extender set but", nim, "has no extensions.")
     }
   }
-  ## reorient?
-  if (nim@"reoriented") {
-    data <- as.vector(inverseReorient(nim))
-  } else {
-    data <- as.vector(nim@.Data)
-  }
+
   ## Write image file...
   if (verbose) {
     cat("  writing data at byte =", seek(fid), fill=TRUE)
   }
+
   switch(as.character(nim@"datatype"),
          "2" = writeBin(as.integer(data), fid, size=nim@"bitpix"/8),
          "4" = writeBin(as.integer(data), fid, size=nim@"bitpix"/8),

cran-comments.md

@@ -1,16 +1,10 @@
 ## Test environments
-* local OS X install, R 3.6.0
-* ubuntu 14.04 (on travis-ci), R 3.6.0
-* win-builder (devel and release)
+* local R installation, R 3.6.3
+* ubuntu 16.04 (on travis-ci), R 3.6.3
+* win-builder (devel)
 
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note
 
 * This is a new release.
-
----
-
-Size of tarball has been large for many years with `oro.nifti` - images in vignette are large. 
-
-"Package has a VignetteBuilder field but no prebuilt vignette index.", which is not a concerning note as one of the vignettes is really an `rticles` Rmd file.