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182 changes: 182 additions & 0 deletions
182
...nelia/render/client/newsolver/solvers/intensity/AffineIntensityCorrectionBlockWorker.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,182 @@ | ||
| package org.janelia.render.client.newsolver.solvers.intensity; | ||
|
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| import mpicbg.models.Affine1D; | ||
| import mpicbg.models.Model; | ||
| import mpicbg.models.NoninvertibleModelException; | ||
| import net.imglib2.util.ValuePair; | ||
| import org.janelia.alignment.filter.FilterSpec; | ||
| import org.janelia.alignment.filter.IntensityMap8BitFilter; | ||
| import org.janelia.alignment.match.CanvasMatches; | ||
| import org.janelia.alignment.spec.ResolvedTileSpecCollection; | ||
| import org.janelia.alignment.spec.TileSpec; | ||
| import org.janelia.alignment.spec.stack.StackMetaData; | ||
| import org.janelia.alignment.util.ImageProcessorCache; | ||
| import org.janelia.render.client.RenderDataClient; | ||
| import org.janelia.render.client.intensityadjust.AdjustBlock; | ||
| import org.janelia.render.client.intensityadjust.AffineIntensityCorrectionStrategy; | ||
| import org.janelia.render.client.intensityadjust.IntensityCorrectionStrategy; | ||
| import org.janelia.render.client.intensityadjust.MinimalTileSpecWrapper; | ||
| import org.janelia.render.client.intensityadjust.virtual.OnTheFlyIntensity; | ||
| import org.janelia.render.client.newsolver.BlockData; | ||
| import org.janelia.render.client.newsolver.blockfactories.BlockFactory; | ||
| import org.janelia.render.client.newsolver.blocksolveparameters.FIBSEMIntensityCorrectionParameters; | ||
| import org.janelia.render.client.newsolver.solvers.Worker; | ||
| import org.janelia.render.client.parameter.IntensityAdjustParameters; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
|
|
||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
| import java.util.concurrent.ExecutionException; | ||
| import java.util.stream.Collectors; | ||
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| public class AffineIntensityCorrectionBlockWorker<M extends Model<M> & Affine1D<M>, F extends BlockFactory<F>> | ||
| extends Worker<M, M, FIBSEMIntensityCorrectionParameters<M>, F> { | ||
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| private final FIBSEMIntensityCorrectionParameters<M> parameters; | ||
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| public AffineIntensityCorrectionBlockWorker( | ||
| final BlockData<M, M, FIBSEMIntensityCorrectionParameters<M>, F> blockData, | ||
| final int startId, | ||
| final int numThreads) throws IOException { | ||
| super(startId, blockData, numThreads); | ||
| parameters = blockData.solveTypeParameters(); | ||
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| if (parameters.intensityCorrectedFilterStack() != null) { | ||
| final StackMetaData stackMetaData = renderDataClient.getStackMetaData(renderStack); | ||
| renderDataClient.setupDerivedStack(stackMetaData, parameters.intensityCorrectedFilterStack()); | ||
| } | ||
| } | ||
|
|
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| /** | ||
| * runs the Worker | ||
| */ | ||
| @Override | ||
| public void run() throws IOException, ExecutionException, InterruptedException, NoninvertibleModelException { | ||
|
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| // TODO: blockData.idToTileSpec() already resolved? | ||
| final ResolvedTileSpecCollection resolvedTileSpecs = getResolvedTileSpecs(); | ||
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| // if specified, use match collection to determine patch pairs instead of tile bounds w/distanceZ | ||
| final List<CanvasMatches> tilePairs; | ||
| if (parameters.matchCollection() != null) { | ||
| tilePairs = getMatchPairsFromCollection(parameters.matchCollection()); | ||
| } else { | ||
| tilePairs = new ArrayList<>(); | ||
| } | ||
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| deriveAndStoreIntensityFilterData(renderDataClient, resolvedTileSpecs, tilePairs); | ||
| LOG.info("AffineIntensityCorrectionBlockWorker: exit, minZ={}, maxZ={}", blockData.minZ(), blockData.maxZ()); | ||
| } | ||
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| private List<CanvasMatches> getMatchPairsFromCollection(final String matchCollection) throws IOException { | ||
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| final RenderDataClient matchClient = new RenderDataClient(renderDataClient.getBaseDataUrl(), renderDataClient.getOwner(), matchCollection); | ||
| final List<CanvasMatches> tilePairs = new ArrayList<>(); | ||
| final Set<String> alreadyConsidered = new HashSet<>(); | ||
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| for (final TileSpec tileSpec : blockData.idToTileSpec().values()) { | ||
| final String pGroupId = tileSpec.getLayout().getSectionId(); | ||
| final boolean isInBlock = blockData.idToTileSpec().containsKey(pGroupId); | ||
| if (!alreadyConsidered.contains(pGroupId) && isInBlock) { | ||
| for (final CanvasMatches pair : matchClient.getMatchesWithPGroupId(pGroupId, true)) { | ||
| if (blockData.idToTileSpec().containsKey(pair.getqId())) | ||
| tilePairs.add(pair); | ||
| } | ||
| alreadyConsidered.add(pGroupId); | ||
| } | ||
| } | ||
| return tilePairs; | ||
| } | ||
|
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| private ResolvedTileSpecCollection getResolvedTileSpecs() { | ||
| final ResolvedTileSpecCollection resolvedTiles; | ||
| try { | ||
| if (blockData.minZ() == blockData.maxZ()) { | ||
| resolvedTiles = renderDataClient.getResolvedTiles(renderStack, (double) blockData.minZ()); | ||
| } else { | ||
| resolvedTiles = renderDataClient.getResolvedTilesForZRange(renderStack, (double) blockData.minZ(), (double) blockData.maxZ()); | ||
| } | ||
| } catch (final IOException e) { | ||
| LOG.error("Error getting resolved tiles for stack {} and z range {}-{}", renderStack, blockData.minZ(), blockData.maxZ()); | ||
| throw new RuntimeException(e); | ||
| } | ||
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| final Set<String> outOfBlockIds = resolvedTiles.getTileIds(); | ||
| outOfBlockIds.removeAll(blockData.idToTileSpec().keySet()); | ||
| resolvedTiles.removeTileSpecs(outOfBlockIds); | ||
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| return resolvedTiles; | ||
| } | ||
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| protected void deriveAndStoreIntensityFilterData( | ||
| final RenderDataClient dataClient, | ||
| final ResolvedTileSpecCollection resolvedTiles, | ||
| final List<CanvasMatches> tilePairs) throws ExecutionException, InterruptedException, IOException { | ||
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| LOG.info("deriveAndStoreIntensityFilterData: entry"); | ||
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| if (resolvedTiles.getTileCount() > 1) { | ||
| final long maxCachedPixels = parameters.maxNumberOfCachedPixels(); | ||
| final ImageProcessorCache imageProcessorCache = (maxCachedPixels == 0) | ||
| ? ImageProcessorCache.DISABLED_CACHE | ||
| : new ImageProcessorCache(parameters.maxNumberOfCachedPixels(), true, false); | ||
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| final List<MinimalTileSpecWrapper> wrappedTiles = AdjustBlock.wrapTileSpecs(resolvedTiles); | ||
| final IntensityCorrectionStrategy strategy = new AffineIntensityCorrectionStrategy(parameters.lambdaTranslation(), parameters.lambdaIdentity()); | ||
| final List<OnTheFlyIntensity> corrected; | ||
|
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| if (!tilePairs.isEmpty()) { | ||
| final List<ValuePair<MinimalTileSpecWrapper, MinimalTileSpecWrapper>> patchPairs = | ||
| tilePairs.stream() | ||
| .map(tp -> new ValuePair<>(resolvedTiles.getTileSpec(tp.getpId()), resolvedTiles.getTileSpec(tp.getqId()))) | ||
| .filter(vp -> (vp.getA() != null) && (vp.getB() != null)) | ||
| .map(vp -> new ValuePair<>(new MinimalTileSpecWrapper(vp.getA()), new MinimalTileSpecWrapper(vp.getB()))) | ||
| .collect(Collectors.toList()); | ||
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| corrected = AdjustBlock.correctIntensitiesForPatchPairs(patchPairs, | ||
| parameters.renderScale(), | ||
| imageProcessorCache, | ||
| parameters.numCoefficients(), | ||
| strategy, | ||
| numThreads); | ||
| } else { | ||
| corrected = AdjustBlock.correctIntensitiesForSliceTiles(wrappedTiles, | ||
| parameters.renderScale(), | ||
| parameters.zDistance(), | ||
| imageProcessorCache, | ||
| parameters.numCoefficients(), | ||
| strategy, | ||
| numThreads); | ||
| } | ||
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| for (final OnTheFlyIntensity onTheFlyIntensity : corrected) { | ||
| final String tileId = onTheFlyIntensity.getMinimalTileSpecWrapper().getTileId(); | ||
| final TileSpec tileSpec = resolvedTiles.getTileSpec(tileId); | ||
| final IntensityMap8BitFilter filter = onTheFlyIntensity.toFilter(); | ||
| final FilterSpec filterSpec = new FilterSpec(filter.getClass().getName(), filter.toParametersMap()); | ||
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| tileSpec.setFilterSpec(filterSpec); | ||
| tileSpec.convertSingleChannelSpecToLegacyForm(); | ||
| } | ||
| } else { | ||
| final String tileCountMsg = resolvedTiles.getTileCount() == 1 ? "1 tile" : "0 tiles"; | ||
| LOG.info("deriveAndStoreIntensityFilterData: skipping correction because collection contains {}", tileCountMsg); | ||
| } | ||
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| dataClient.saveResolvedTiles(resolvedTiles, parameters.intensityCorrectedFilterStack(), null); | ||
| } | ||
|
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| /** | ||
| * @return - the result(s) of the solve, multiple ones if they were not connected | ||
| */ | ||
| @Override | ||
| public List<BlockData<M, M, FIBSEMIntensityCorrectionParameters<M>, F>> getBlockDataList() { | ||
| return null; | ||
| } | ||
|
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| private static final Logger LOG = LoggerFactory.getLogger(Worker.class); | ||
| } |
28 changes: 28 additions & 0 deletions
28
...java/org/janelia/render/client/newsolver/solvers/intensity/IntensityBlockDataWrapper.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| package org.janelia.render.client.newsolver.solvers.intensity; | ||
|
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| import mpicbg.models.Affine1D; | ||
| import mpicbg.models.Model; | ||
| import mpicbg.models.Tile; | ||
| import org.janelia.render.client.newsolver.BlockData; | ||
| import org.janelia.render.client.newsolver.blockfactories.BlockFactory; | ||
| import org.janelia.render.client.newsolver.blocksolveparameters.FIBSEMIntensityCorrectionParameters; | ||
|
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| import java.util.HashMap; | ||
| import java.util.Map; | ||
|
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| /** | ||
| * Wrapper for all data needed to run the intensity correction solver | ||
| */ | ||
| public class IntensityBlockDataWrapper<M extends Model<M> & Affine1D<M>, F extends BlockFactory<F>> { | ||
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| final BlockData<M, ?, FIBSEMIntensityCorrectionParameters<M>, F> blockData; | ||
| final private Map<String, Tile<M>> idToTile = new HashMap<>(); | ||
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| public IntensityBlockDataWrapper(final BlockData<M, ?, FIBSEMIntensityCorrectionParameters<M>, F> blockData) { | ||
| this.blockData = blockData; | ||
| } | ||
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| public BlockData<M, ?, FIBSEMIntensityCorrectionParameters<M>, F> blockData() { return blockData; } | ||
| public Map<String, Tile<M>> idToTile() { return idToTile; } | ||
| } |
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