Deal with (=explicitly ignore) string annotations

Author: minnerbe

src/main/java/cmd/PairwiseSectionAligner.java

@@ -203,10 +203,12 @@ public Void call() throws Exception {
 				logger.debug("Gene annotation '{}' was found for {}. Omitting.", stdevLabel, datasetName);
 				continue;
 			}
+			if (numGenes == 0) {
+				continue;
+			}
 
-			final boolean computeStdev = (numGenes > 0 && entropyPath == null);
 			final RandomAccessibleInterval<DoubleType> entropyValues;
-			if (computeStdev) {
+			if (entropyPath == null) {
 				logger.info("Computing standard deviation of genes for {} (may take a while)", datasetName);
 				entropyValues = ExtractGeneLists.computeOrderedEntropy(stData.data(), Entropy.STDEV, numThreads);
 			} else {
@@ -215,7 +217,7 @@ public Void call() throws Exception {
 			}
 			stData.data().getGeneAnnotations().put(stdevLabel, entropyValues);
 
-			if (computeStdev) {
+			if (entropyPath == null) {
 				try {
 					container.openDataset(datasetName).updateStoredGeneAnnotations(stData.data().getGeneAnnotations());
 				} catch (IOException e) {

src/main/java/io/SpatialDataIO.java

@@ -165,11 +165,21 @@ public STDataAssembly readData() throws IOException {
 		AffineTransform2D transform = new AffineTransform2D();
 		readAndSetTransformation(reader, transform, transformFieldName);
 
-		for (final String annotationLabel : detectAnnotations(reader))
-			stData.getAnnotations().put(annotationLabel, readAnnotations(reader, annotationLabel));
+		for (final String annotationLabel : detectAnnotations(reader)) {
+			try {
+				stData.getAnnotations().put(annotationLabel, readAnnotations(reader, annotationLabel));
+			} catch (Exception e) {
+				logger.warn("Could not read annotation '{}'. Skipping", annotationLabel);
+			}
+		}
 
-		for (final String geneAnnotationLabel : detectGeneAnnotations(reader))
-			stData.getGeneAnnotations().put(geneAnnotationLabel, readGeneAnnotations(reader, geneAnnotationLabel));
+		for (final String geneAnnotationLabel : detectGeneAnnotations(reader)) {
+			try {
+				stData.getGeneAnnotations().put(geneAnnotationLabel, readGeneAnnotations(reader, geneAnnotationLabel));
+			} catch (Exception e) {
+				logger.warn("Could not read annotation '{}'. Skipping", geneAnnotationLabel);
+			}
+		}
 
 		logger.debug("Loading took {} ms.", System.currentTimeMillis() - time);
 		logger.debug("Metadata: dims={}, numLocations={}, numGenes={}, size(locations)={}, size(exprValues)={}",