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Merge pull request #199 from saalfeldlab/fix-fragment-segment-assignm…
…ent-deserialization Serialize initial lut supplier in paintera project
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49 changes: 49 additions & 0 deletions
49
...b/paintera/serialization/assignments/N5FragmentSegmentAssignmentInitialLutSerializer.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,49 @@ | ||
| package org.janelia.saalfeldlab.paintera.serialization.assignments; | ||
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| import com.google.gson.JsonDeserializationContext; | ||
| import com.google.gson.JsonElement; | ||
| import com.google.gson.JsonObject; | ||
| import com.google.gson.JsonParseException; | ||
| import com.google.gson.JsonSerializationContext; | ||
| import org.janelia.saalfeldlab.paintera.data.n5.N5Meta; | ||
| import org.janelia.saalfeldlab.paintera.data.n5.ReflectionException; | ||
| import org.janelia.saalfeldlab.paintera.serialization.PainteraSerialization; | ||
| import org.janelia.saalfeldlab.paintera.serialization.SerializationHelpers; | ||
| import org.janelia.saalfeldlab.util.n5.N5FragmentSegmentAssignmentInitialLut; | ||
| import org.janelia.saalfeldlab.util.n5.N5FragmentSegmentAssignmentPersister; | ||
| import org.scijava.plugin.Plugin; | ||
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| import java.io.IOException; | ||
| import java.lang.reflect.Type; | ||
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| @Plugin(type = PainteraSerialization.PainteraAdapter.class) | ||
| public class N5FragmentSegmentAssignmentInitialLutSerializer implements | ||
| PainteraSerialization.PainteraAdapter<N5FragmentSegmentAssignmentInitialLut> | ||
| { | ||
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| private static final String N5_META_KEY = "N5"; | ||
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| @Override | ||
| public N5FragmentSegmentAssignmentInitialLut deserialize(JsonElement jsonElement, Type type, JsonDeserializationContext context) throws JsonParseException { | ||
| try { | ||
| final N5Meta meta = SerializationHelpers.deserializeFromClassInfo(jsonElement.getAsJsonObject().get(N5_META_KEY).getAsJsonObject(), context); | ||
| return new N5FragmentSegmentAssignmentInitialLut(meta); | ||
| } catch (ClassNotFoundException e) { | ||
| throw new JsonParseException(e); | ||
| } | ||
| } | ||
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| @Override | ||
| public JsonElement serialize(N5FragmentSegmentAssignmentInitialLut src, Type type, JsonSerializationContext context) { | ||
| final JsonObject map = new JsonObject(); | ||
| map.add(N5_META_KEY, SerializationHelpers.serializeWithClassInfo(src.getMeta(), context)); | ||
| return map; | ||
| } | ||
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| @Override | ||
| public Class<N5FragmentSegmentAssignmentInitialLut> getTargetClass() { | ||
| return N5FragmentSegmentAssignmentInitialLut.class; | ||
| } | ||
| } |
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80 changes: 80 additions & 0 deletions
80
src/main/java/org/janelia/saalfeldlab/util/n5/N5FragmentSegmentAssignmentInitialLut.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| package org.janelia.saalfeldlab.util.n5; | ||
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| import com.google.gson.annotations.Expose; | ||
| import gnu.trove.map.TLongLongMap; | ||
| import gnu.trove.map.hash.TLongLongHashMap; | ||
| import net.imglib2.Cursor; | ||
| import net.imglib2.RandomAccessibleInterval; | ||
| import net.imglib2.converter.Converters; | ||
| import net.imglib2.type.NativeType; | ||
| import net.imglib2.type.numeric.IntegerType; | ||
| import net.imglib2.type.numeric.integer.UnsignedLongType; | ||
| import net.imglib2.view.Views; | ||
| import org.janelia.saalfeldlab.n5.DataType; | ||
| import org.janelia.saalfeldlab.n5.N5Reader; | ||
| import org.janelia.saalfeldlab.n5.imglib2.N5Utils; | ||
| import org.janelia.saalfeldlab.paintera.data.n5.N5Meta; | ||
| import org.janelia.saalfeldlab.paintera.data.n5.ReflectionException; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| import java.io.IOException; | ||
| import java.lang.invoke.MethodHandles; | ||
| import java.util.function.Supplier; | ||
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| public class N5FragmentSegmentAssignmentInitialLut implements Supplier<TLongLongMap> { | ||
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| private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass()); | ||
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| @Expose | ||
| private final N5Meta meta; | ||
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| public N5FragmentSegmentAssignmentInitialLut(final N5Reader container, final String dataset) throws ReflectionException { | ||
| this(N5Meta.fromReader(container, dataset)); | ||
| } | ||
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| public N5FragmentSegmentAssignmentInitialLut(final N5Meta meta) { | ||
| this.meta = meta; | ||
| } | ||
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| public N5Meta getMeta() { | ||
| return this.meta; | ||
| } | ||
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| @Override | ||
| public TLongLongMap get() { | ||
| try { | ||
| RandomAccessibleInterval<UnsignedLongType> data = openDatasetSafe(meta.reader(), meta.dataset()); | ||
| final long[] keys = new long[(int) data.dimension(0)]; | ||
| final long[] values = new long[keys.length]; | ||
| LOG.debug("Found {} assignments", keys.length); | ||
| final Cursor<UnsignedLongType> keyCursor = Views.flatIterable(Views.hyperSlice(data, 1, 0L)).cursor(); | ||
| final Cursor<UnsignedLongType> valueCursor = Views.flatIterable(Views.hyperSlice(data, 1, 1L)).cursor(); | ||
| for (int i = 0; i < keys.length; ++i) { | ||
| keys[i] = keyCursor.next().getIntegerLong(); | ||
| values[i] = valueCursor.next().getIntegerLong(); | ||
| } | ||
| return new TLongLongHashMap(keys, values); | ||
| } catch (IOException e) { | ||
| LOG.debug("Exception while trying to return initial lut from N5", e); | ||
| LOG.error("Unable to read initial lut from {} -- returning empty map", meta, e); | ||
| return new TLongLongHashMap(); | ||
| } | ||
| } | ||
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| private static RandomAccessibleInterval<UnsignedLongType> openDatasetSafe( | ||
| final N5Reader reader, | ||
| final String dataset | ||
| ) throws IOException { | ||
| return DataType.UINT64.equals(reader.getDatasetAttributes(dataset).getDataType()) | ||
| ? N5Utils.open(reader, dataset) | ||
| : openAnyIntegerTypeAsUnsignedLongType(reader, dataset); | ||
| } | ||
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| private static <T extends IntegerType<T> & NativeType<T>> RandomAccessibleInterval<UnsignedLongType> openAnyIntegerTypeAsUnsignedLongType( | ||
| final N5Reader reader, | ||
| final String dataset | ||
| ) throws IOException { | ||
| return Converters.convert(N5Utils.<T>open(reader, dataset), (s, t) -> t.setInteger(s.getIntegerLong()), new UnsignedLongType()); | ||
| } | ||
| } |
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