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Add fall-back serializers for RawSourceState
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124 changes: 124 additions & 0 deletions
124
...n/kotlin/org/janelia/saalfeldlab/paintera/state/raw/RawSourceStateFallbackDeserializer.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,124 @@ | ||
| package org.janelia.saalfeldlab.paintera.state.raw | ||
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| import bdv.viewer.Interpolation | ||
| import com.google.gson.JsonDeserializationContext | ||
| import com.google.gson.JsonDeserializer | ||
| import com.google.gson.JsonElement | ||
| import com.google.gson.JsonObject | ||
| import net.imglib2.realtransform.AffineTransform3D | ||
| import net.imglib2.type.NativeType | ||
| import net.imglib2.type.numeric.ARGBType | ||
| import net.imglib2.type.numeric.RealType | ||
| import net.imglib2.type.volatiles.AbstractVolatileRealType | ||
| import org.janelia.saalfeldlab.paintera.composition.Composite | ||
| import org.janelia.saalfeldlab.paintera.data.n5.N5DataSource | ||
| import org.janelia.saalfeldlab.paintera.data.n5.N5Meta | ||
| import org.janelia.saalfeldlab.paintera.serialization.GsonExtensions | ||
| import org.janelia.saalfeldlab.paintera.serialization.SerializationHelpers | ||
| import org.janelia.saalfeldlab.paintera.serialization.StatefulSerializer | ||
| import org.janelia.saalfeldlab.paintera.serialization.sourcestate.LabelSourceStateDeserializer | ||
| import org.janelia.saalfeldlab.paintera.serialization.sourcestate.SourceStateSerialization | ||
| import org.janelia.saalfeldlab.paintera.state.RawSourceState | ||
| import org.janelia.saalfeldlab.paintera.state.SourceState | ||
| import org.janelia.saalfeldlab.paintera.state.raw.n5.N5BackendRaw | ||
| import org.janelia.saalfeldlab.util.Colors | ||
| import org.scijava.plugin.Plugin | ||
| import org.slf4j.LoggerFactory | ||
| import java.lang.invoke.MethodHandles | ||
| import java.lang.reflect.Type | ||
| import java.util.function.IntFunction | ||
| import java.util.function.Supplier | ||
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| class RawSourceStateFallbackDeserializer<D, T>(private val arguments: StatefulSerializer.Arguments) : JsonDeserializer<SourceState<*, *>> | ||
| where D: RealType<D>, | ||
| D: NativeType<D>, | ||
| T: AbstractVolatileRealType<D, T>, | ||
| T: NativeType<T> { | ||
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| private val fallbackDeserializer: LabelSourceStateDeserializer<*> = LabelSourceStateDeserializer.create(arguments) | ||
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| override fun deserialize(json: JsonElement, typeOfT: Type, context: JsonDeserializationContext): SourceState<*, *> { | ||
| return json.getN5MetaAndTransform(context)?.let { (meta, transform) -> | ||
| val (resolution, offset) = transform.toOffsetAndResolution() | ||
| val backend = N5BackendRaw<D, T>( | ||
| meta.writer, | ||
| meta.dataset, | ||
| resolution, | ||
| offset, | ||
| arguments.viewer.queue, | ||
| 0, | ||
| with (GsonExtensions) { json.getStringProperty("name") } ?: "<N/A>") | ||
| ConnectomicsRawState(backend) | ||
| .also { LOG.debug("Successfully converted state {} into {}", json, it) } | ||
| .also { s -> SerializationHelpers.deserializeFromClassInfo<Composite<ARGBType, ARGBType>>(json.asJsonObject, context, "compositeType", "composite")?.let { s.composite = it } } | ||
| // TODO what about other converter properties like user-defined colors? | ||
| .also { s -> with (GsonExtensions) { s.updateConverterSettings(json.getJsonObject("converter")) } } | ||
| .also { s -> with (GsonExtensions) { json.getProperty("interpolation")?.let { context.deserialize<Interpolation>(it, Interpolation::class.java) }?.let { s.interpolation = it } } } | ||
| .also { s -> with (GsonExtensions) { json.getBooleanProperty("isVisible") }?.let { s.isVisible = it } } | ||
| } ?: run { | ||
| // TODO should this throw an exception instead? could be handled downstream with fall-back and a warning dialog | ||
| LOG.warn( | ||
| "Unable to de-serialize/convert deprecated `{}' into `{}', falling back using `{}'. Support for `{}' has been deprecated and may be removed in the future.", | ||
| RawSourceState::class.java.simpleName, | ||
| ConnectomicsRawState::class.java.simpleName, | ||
| LabelSourceStateDeserializer::class.java.simpleName, | ||
| RawSourceState::class.java.simpleName) | ||
| fallbackDeserializer.deserialize(json, typeOfT, context) | ||
| } | ||
| } | ||
|
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| companion object { | ||
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| private val LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass()) | ||
|
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| private fun JsonElement.getN5MetaAndTransform( | ||
| context: JsonDeserializationContext, | ||
| typeKey: String = SourceStateSerialization.SOURCE_TYPE_KEY, | ||
| dataKey: String = SourceStateSerialization.SOURCE_KEY, | ||
| metaTypeKey: String = "metaType", | ||
| metaKey: String = "meta", | ||
| transformKey: String = "transform"): Pair<N5Meta, AffineTransform3D>? = with(GsonExtensions) { | ||
| val type = getStringProperty(typeKey) | ||
| val data = getJsonObject(dataKey) | ||
| if (N5DataSource::class.java.name == type) | ||
| Pair( | ||
| context.deserialize(data?.get(metaKey), Class.forName(data?.getStringProperty(metaTypeKey))) as N5Meta, | ||
| context.deserialize(data?.get(transformKey), AffineTransform3D::class.java)) | ||
| else | ||
| null | ||
| } | ||
|
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| private fun AffineTransform3D.toOffsetAndResolution() = Pair( | ||
| DoubleArray(3) { this[it, it] }, | ||
| DoubleArray(3) { this[it, 3] }) | ||
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| private fun ConnectomicsRawState<*, *>.updateConverterSettings(json: JsonObject?) = json?.let { j -> | ||
| val c = converter() | ||
| with (GsonExtensions) { | ||
| j.getDoubleProperty("alpha")?.let { c.alphaProperty().value = it } | ||
| j.getDoubleProperty("min")?.let { c.setMin(it) } | ||
| j.getDoubleProperty("max")?.let { c.setMax(it) } | ||
| j.getStringProperty("color")?.let { c.setColor(Colors.toARGBType(it)) } | ||
| } | ||
| } | ||
| } | ||
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| @Plugin(type = StatefulSerializer.DeserializerFactory::class) | ||
| class Factory<D, T>: StatefulSerializer.DeserializerFactory<SourceState<*, *>, RawSourceStateFallbackDeserializer<D, T>> | ||
| where D: RealType<D>, | ||
| D: NativeType<D>, | ||
| T: AbstractVolatileRealType<D, T>, | ||
| T: NativeType<T>{ | ||
| override fun createDeserializer( | ||
| arguments: StatefulSerializer.Arguments, | ||
| projectDirectory: Supplier<String>, | ||
| dependencyFromIndex: IntFunction<SourceState<*, *>> | ||
| ): RawSourceStateFallbackDeserializer<D, T> = | ||
| RawSourceStateFallbackDeserializer(arguments) | ||
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| override fun getTargetClass(): Class<SourceState<*, *>> = RawSourceState::class.java as Class<SourceState<*, *>> | ||
|
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| } | ||
| } | ||
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