Merge pull request #126 from tischi/write_axis_tags

Added axes serialization to json for export
ilastik · Jun 6, 2024 · 93a62c2 · 93a62c2
2 parents 661310c + 2722a5f
commit 93a62c2
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diff --git a/src/main/java/org/ilastik/ilastik4ij/hdf5/Hdf5.java b/src/main/java/org/ilastik/ilastik4ij/hdf5/Hdf5.java
@@ -67,6 +67,7 @@
 import static org.ilastik.ilastik4ij.util.ImgUtils.DEFAULT_AXES;
 import static org.ilastik.ilastik4ij.util.ImgUtils.argbToMultiChannel;
 import static org.ilastik.ilastik4ij.util.ImgUtils.axesOf;
+import static org.ilastik.ilastik4ij.util.ImgUtils.axesToJSON;
 import static org.ilastik.ilastik4ij.util.ImgUtils.inputBlockDims;
 import static org.ilastik.ilastik4ij.util.ImgUtils.outputDims;
 import static org.ilastik.ilastik4ij.util.ImgUtils.reversed;
@@ -286,6 +287,9 @@ public static <T extends NativeType<T>> void writeDataset(
                      reversed(chunkDims),
                      compressionLevel)) {
 
+            // Add axes tags
+            writer.string().setAttr(dataset.getDataSetPath(), "axistags", axesToJSON(axes));
+
             callback.accept(0L);
 
             while (gridCursor.hasNext()) {

diff --git a/src/main/java/org/ilastik/ilastik4ij/util/ImgUtils.java b/src/main/java/org/ilastik/ilastik4ij/util/ImgUtils.java
@@ -325,6 +325,41 @@ public static List<AxisType> parseAxes(String json) {
         return axes;
     }
 
+    public static String axesToJSON(List<AxisType> axes)
+    {
+        JSONArray jsonAxesArray = new JSONArray();
+        List<AxisType> axes_for_serialization = new ArrayList<>(axes);
+        Collections.reverse(axes_for_serialization);
+        for (AxisType axis : axes_for_serialization)
+        {
+            JSONObject jsonAxis = new JSONObject();
+            String label = axis.getLabel().toLowerCase();
+            int vigraType;
+            String vigraKey;
+            if (axis.isSpatial()){
+                vigraType = 2;
+                vigraKey = label;
+            } else if (label.equals("time")) {
+                vigraType = 8;
+                vigraKey = "t";
+            } else if (label.equals("channel")) {
+                vigraType = 1;
+                vigraKey = "c";
+            } else {
+                throw new IllegalArgumentException(
+                        String.format("Unknown axis type found with label %s.", label));
+            }
+            jsonAxis.put("key", vigraKey);
+            jsonAxis.put("typeFlags", vigraType);
+            jsonAxesArray.put(jsonAxis);
+        }
+
+        JSONObject root = new JSONObject();
+        root.put("axes", jsonAxesArray);
+
+        return root.toString();
+    }
+
     /**
      * Treat alpha, red, green, and blue values in {@link ARGBType} image
      * as a separate, last channel dimension.