v1.2.2 number format bugfix

kuwisdelu · Oct 25, 2024 · 13baf2d · 13baf2d
1 parent 01a688e
commit 13baf2d
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Showing 3 changed files with 16 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CardinalIO
 Type: Package
 Title: Read and write mass spectrometry imaging files
-Version: 1.2.1
+Version: 1.2.2
 Date: 2023-8-29
 Authors@R: person("Kylie Ariel", "Bemis",
 	email = "[email protected]",

diff --git a/NEWS b/NEWS
@@ -1,4 +1,12 @@
 
+CHANGES IN VERSION 1.2.2 [2024-10-24]
+------------------------------------
+
+BUG FIXES
+
+    o Fix writing scientific notation to imzML output
+        (note: only affected parsing, not precision)
+
 CHANGES IN VERSION 1.2.1 [2024-5-7]
 ------------------------------------
 

diff --git a/R/writeImzML.R b/R/writeImzML.R
@@ -32,7 +32,7 @@ setMethod("writeImzML", "ImzMeta",
 	# process positions
 	if ( !is.null(positions) )
 	{
-		positions <- as.data.frame(apply(positions, 2L, as.character))
+		positions <- as.data.frame(apply(positions, 2L, .format_values))
 		if ( ncol(positions) == 2L ) {
 			names(positions) <- c("position x", "position y")
 		} else if ( ncol(positions) == 3L ) {
@@ -212,7 +212,7 @@ setMethod("writeImzML", "ImzMeta",
 	mzArrays[["external array length"]] <- rep_len(mza$extent, n)
 	mzArrays[["external encoded length"]] <- rep_len(xlen, n)
 	mzArrays[["binary data type"]] <- rep_len(mza$type, n)
-	mzArrays[] <- lapply(mzArrays, as.character)
+	mzArrays[] <- lapply(mzArrays, .format_values)
 	# get intensity metadata
 	intensityArrays <- data.frame(row.names=seq_len(n))
 	ia <- as.data.frame(atomdata(intensity))
@@ -221,7 +221,7 @@ setMethod("writeImzML", "ImzMeta",
 	intensityArrays[["external array length"]] <- ia$extent
 	intensityArrays[["external encoded length"]] <- xlen
 	intensityArrays[["binary data type"]] <- ia$type
-	intensityArrays[] <- lapply(intensityArrays, as.character)
+	intensityArrays[] <- lapply(intensityArrays, .format_values)
 	# get checksum and uuid as 8-4-4-4-12 formatted string
 	path <- path(mz)
 	checksum <- checksum(path, algo=algo)
@@ -271,6 +271,10 @@ setMethod("writeImzML", "ImzMeta",
 	metadata
 }
 
+.format_values <- function(x) {
+	ifelse(is.na(x), NA_character_, format(x, scientific=FALSE))
+}
+
 #### Deparse generic imzML tags ####
 ## ----------------------------------