FeatureCalculation: Restore axis information in created bitmasks Fixes …

…#506
knime-ip · Aug 14, 2018 · 6ba5651 · 6ba5651
1 parent 1198fb3
commit 6ba5651
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Showing 3 changed files with 32 additions and 15 deletions.
diff --git a/org.knime.knip.features/src/org/knime/knip/features/groups/AbstractFeatureSetGroup.java b/org.knime.knip.features/src/org/knime/knip/features/groups/AbstractFeatureSetGroup.java
@@ -55,6 +55,7 @@
 import java.util.Map;
 
 import net.imagej.ImgPlus;
+import net.imagej.axis.CalibratedAxis;
 import net.imagej.ops.OpEnvironment;
 import net.imagej.ops.special.computer.AbstractUnaryComputerOp;
 import net.imglib2.img.Img;
@@ -84,7 +85,7 @@
 /**
  * FIXME: Design of FeatureGroups is really weak. However, we can redesign it
  * whenever we have more time, without destroying backwards compatibility.
- * 
+ *
  * @author Christian Dietz, University of Konstanz
  *
  * @param <L>
@@ -210,13 +211,14 @@ protected <I> List<DataCell> computeOnFeatureSets(final List<FeatureSet<I, O>> s
 
 	protected <L> void appendRegionOptions(final LabelRegion<L> region, final List<DataCell> cells,
 			final ImgPlusCellFactory imgPlusCellFactory, final Map<L, List<L>> dependencies,
-			final boolean appendOverlappingLabels, final OpEnvironment ops) {
+			final boolean appendOverlappingLabels, final OpEnvironment ops, final CalibratedAxis[] axes) {
 		if (imgPlusCellFactory != null) {
 			@SuppressWarnings("unchecked")
-			Img<BitType> bitmask = (Img<BitType>) ops.run(LabelRegionToBitmaskConverter.class, region);
+			final Img<BitType> bitmask = (Img<BitType>) ops.run(LabelRegionToBitmaskConverter.class, region);
 			try {
-				cells.add(imgPlusCellFactory.createCell(new ImgPlus<BitType>(bitmask)));
-			} catch (IOException exc) {
+				final ImgPlus<BitType> imgPlus = new ImgPlus<>(bitmask, "bitmask", axes);
+				cells.add(imgPlusCellFactory.createCell(imgPlus));
+			} catch (final IOException exc) {
 				KNIPGateway.log()
 						.warn("Could not create bitmask for label " + region.toString() + ". Inserted missing cell.");
 				cells.add(DataType.getMissingCell());

diff --git a/org.knime.knip.features/src/org/knime/knip/features/groups/ImgLabelingFeatureSetGroup.java b/org.knime.knip.features/src/org/knime/knip/features/groups/ImgLabelingFeatureSetGroup.java
@@ -54,6 +54,7 @@
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.Future;
 
+import net.imagej.axis.CalibratedAxis;
 import net.imagej.ops.slice.SlicesII;
 import net.imagej.ops.special.computer.UnaryComputerOp;
 import net.imglib2.Cursor;
@@ -78,6 +79,7 @@
 import org.knime.knip.base.data.labeling.LabelingValue;
 import org.knime.knip.base.node.nodesettings.SettingsModelDimSelection;
 import org.knime.knip.core.KNIPGateway;
+import org.knime.knip.core.data.img.LabelingMetadata;
 import org.knime.knip.core.ops.misc.LabelingDependency;
 import org.knime.knip.core.ui.imgviewer.events.RulebasedLabelFilter;
 import org.knime.knip.features.DataRowUtil;
@@ -88,6 +90,7 @@
 /**
  * FIXME: Design of FeatureGroups is really weak. However, we can redesign it
  * whenever we have more time, without destroying backwards compatibility.
+ *
  * @author Christian Dietz, University of Konstanz
  *
  * @param <L>
@@ -183,8 +186,9 @@ public void compute(final DataRow row, final DataContainer container) {
 				final RandomAccessibleInterval<LabelingType<L>> labeling = labValue.getLabeling();
 				// here we have to loop!!!
 
+				final LabelingMetadata labelingMetadata = labValue.getLabelingMetadata();
 				final SlicesII<LabelingType<L>> slicer = new SlicesII<>(labeling,
-						dimSelection.getSelectedDimIndices(labValue.getLabelingMetadata()), true);
+						dimSelection.getSelectedDimIndices(labelingMetadata), true);
 
 				final Cursor<RandomAccessibleInterval<LabelingType<L>>> slicingCursor = slicer.cursor();
 
@@ -222,6 +226,11 @@ public void compute(final DataRow row, final DataContainer container) {
 						intervalDef = " Pos[" + Arrays.toString(pos) + "]";
 
 					}
+					final CalibratedAxis[] labelAxes = new CalibratedAxis[dimSelection.getNumSelectedDimLabels()];
+					final int[] selectedIdx = dimSelection.getSelectedDimIndices(labelingMetadata);
+					for (int i = 0; i < selectedIdx.length; i++) {
+						labelAxes[i] = labelingMetadata.axis(selectedIdx[i]);
+					}
 
 					final ArrayList<Future<Pair<String, List<DataCell>>>> futures = new ArrayList<>();
 					for (final LabelRegion<L> region : regions) {
@@ -231,8 +240,8 @@ public void compute(final DataRow row, final DataContainer container) {
 						futures.add(KNIPGateway.threads().run(() -> {
 							final List<DataCell> cells = new ArrayList<>();
 
-								appendRegionOptions(region, cells, imgPlusCellFactory, dependencies,
-										appendOverlappingSegments, ops());
+							appendRegionOptions(region, cells, imgPlusCellFactory, dependencies,
+									appendOverlappingSegments, ops(), labelAxes);
 
 							cells.addAll(computeOnFeatureSets(featureSets, region));
 

diff --git a/org.knime.knip.features/src/org/knime/knip/features/groups/PairedFeatureSetGroup.java b/org.knime.knip.features/src/org/knime/knip/features/groups/PairedFeatureSetGroup.java
@@ -56,6 +56,7 @@
 import java.util.concurrent.Future;
 
 import net.imagej.ImgPlus;
+import net.imagej.axis.CalibratedAxis;
 import net.imagej.ops.slice.SlicesII;
 import net.imagej.ops.special.computer.UnaryComputerOp;
 import net.imglib2.Cursor;
@@ -84,6 +85,7 @@
 import org.knime.knip.base.data.labeling.LabelingValue;
 import org.knime.knip.base.node.nodesettings.SettingsModelDimSelection;
 import org.knime.knip.core.KNIPGateway;
+import org.knime.knip.core.data.img.LabelingMetadata;
 import org.knime.knip.core.ops.misc.LabelingDependency;
 import org.knime.knip.core.ui.imgviewer.events.RulebasedLabelFilter;
 import org.knime.knip.core.util.MiscViews;
@@ -95,7 +97,7 @@
 /**
  * FIXME: Design of FeatureGroups is really weak. However, we can redesign it
  * whenever we have more time, without destroying backwards compatibility.
- * 
+ *
  * @author Christian Dietz, University of Konstanz
  *
  * @param <L>
@@ -213,16 +215,17 @@ public void compute(final DataRow row, final DataContainer container) {
 				final ImgPlus<T> imgPlus = ((ImgPlusValue<T>) imgPlusCell).getImgPlus();
 				RandomAccessibleInterval<LabelingType<L>> labeling = val.getLabeling();
 
+				LabelingMetadata labelingMetadata = val.getLabelingMetadata();
 				if (!Intervals.equalDimensions(imgPlus, labeling)) {
 					KNIPGateway.log().warn("The dimensions of Labeling and Image in Row " + row.getKey()
 							+ " are not compatible. Dimensions of labeling are virtually adjusted to match size.");
 
-					labeling = MiscViews.synchronizeDimensionality(labeling, val.getLabelingMetadata(), imgPlus,
+					labeling = MiscViews.synchronizeDimensionality(labeling, labelingMetadata, imgPlus,
 							imgPlus);
 				}
 
 				final SlicesII<LabelingType<L>> slicerLab = new SlicesII<>(labeling,
-						dimSelection.getSelectedDimIndices(val.getLabelingMetadata()), true);
+						dimSelection.getSelectedDimIndices(labelingMetadata), true);
 
 				final SlicesII<T> slicerImg = new SlicesII<>(imgPlus, dimSelection.getSelectedDimIndices(imgPlus),
 						true);
@@ -268,6 +271,11 @@ public void compute(final DataRow row, final DataContainer container) {
 
 					}
 
+					final CalibratedAxis[] labelAxes = new CalibratedAxis[dimSelection.getNumSelectedDimLabels()];
+					final int[] selectedIdx = dimSelection.getSelectedDimIndices(labelingMetadata);
+					for (int i = 0; i < selectedIdx.length; i++) {
+						labelAxes[i] = labelingMetadata.axis(selectedIdx[i]);
+					}
 					final ArrayList<Future<Pair<String, List<DataCell>>>> futures = new ArrayList<>();
 					for (final LabelRegion<L> region : regions) {
 						if (!labelFilter.getRules().isEmpty() && !labelFilter.isValid(region.getLabel())) {
@@ -277,11 +285,9 @@ public void compute(final DataRow row, final DataContainer container) {
 						futures.add(KNIPGateway.threads().run(() -> {
 							final List<DataCell> cells = new ArrayList<>();
 
-								appendRegionOptions(region, cells, imgPlusCellFactory, dependencies,
-										appendOverlappingSegments, ops());
+							appendRegionOptions(region, cells, imgPlusCellFactory, dependencies,
+									appendOverlappingSegments, ops(), labelAxes);
 
-								cells.addAll(computeOnFeatureSets(regionSets, region));
-								cells.addAll(computeOnFeatureSets(iterableSets, Regions.sample(region, sliceImgPlus)));
 							cells.addAll(computeOnFeatureSets(regionSets, region));
 							cells.addAll(computeOnFeatureSets(iterableSets, Regions.sample(region, sliceImgPlus)));