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add support to load alignment pipeline parameters from URL-based reso…
…urces to facilitate usage in Google Cloud Spark runs
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53 changes: 53 additions & 0 deletions
53
render-app/src/main/java/org/janelia/alignment/util/UrlResourceUtil.java
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| @@ -0,0 +1,53 @@ | ||
| package org.janelia.alignment.util; | ||
|
|
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| import java.io.BufferedInputStream; | ||
| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.io.InputStreamReader; | ||
| import java.io.Reader; | ||
| import java.net.URL; | ||
| import java.net.URLConnection; | ||
| import java.util.zip.GZIPInputStream; | ||
| import java.util.zip.ZipInputStream; | ||
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|
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| /** | ||
| * Shared URL management utilities. | ||
| * | ||
| * @author Eric Trautman | ||
| */ | ||
| public class UrlResourceUtil { | ||
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| public static final UrlResourceUtil DEFAULT_INSTANCE = new UrlResourceUtil(); | ||
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| private final int bufferSize; | ||
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| public UrlResourceUtil() { | ||
| this(DEFAULT_BUFFER_SIZE); | ||
| } | ||
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| public UrlResourceUtil(final int bufferSize) { | ||
| this.bufferSize = bufferSize; | ||
| } | ||
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| public Reader getExtensionBasedReader(final URL url) | ||
| throws IOException { | ||
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| final InputStream inputStream; | ||
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| final URLConnection connection = url.openConnection(); | ||
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| final String path = url.getPath(); | ||
| if (path.endsWith(".gz")) { | ||
| inputStream = new GZIPInputStream(connection.getInputStream()); | ||
| } else if (path.endsWith(".zip")) { | ||
| inputStream = new ZipInputStream(connection.getInputStream()); | ||
| } else { | ||
| inputStream = new BufferedInputStream(connection.getInputStream(), bufferSize); | ||
| } | ||
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|
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| return new InputStreamReader(inputStream); | ||
| } | ||
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| private static final int DEFAULT_BUFFER_SIZE = 65536; | ||
|
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| } |
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156 changes: 156 additions & 0 deletions
156
...rc/main/resources/multisem/wafer_60/pipeline_json/01_match/pipe.01.match-patch-check.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,156 @@ | ||
| { | ||
| "multiProject": { | ||
| "baseDataUrl" : "http://10.40.3.113:8080/render-ws/v1", | ||
| "owner" : "trautmane", "project" : "w60_serial_290_to_299", | ||
| "stackIdWithZ" : { "projectPattern": "^w6._serial_..._to_...$", "zValuesPerBatch": 1 } | ||
| }, | ||
| "pipelineStackGroups": { | ||
| "raw": { "stackPattern": "^w.._s..._r.._d00$" }, | ||
| "aligned": { "stackPattern": "^w.._s..._r.._d00_align$" }, | ||
| "intensityCorrected": { "stackPattern": "^w.._s..._r.._d00_align_ic$" } | ||
| }, | ||
| "pipelineSteps": [ | ||
| "DERIVE_TILE_MATCHES", | ||
| "PATCH_MFOV_MONTAGE_MATCHES", | ||
| "FIND_UNCONNECTED_MFOVS" | ||
| ], | ||
| "matchRunList": [ | ||
| { | ||
| "runName": "montageMfovRun", | ||
| "matchCommon": { | ||
| "maxPairsPerStackBatch" : 30, | ||
| "featureStorage": { "maxFeatureSourceCacheGb": 6 }, | ||
| "maxPeakCacheGb" : 2 | ||
| }, | ||
| "tilePairDerivationParameters": { | ||
| "xyNeighborFactor": 0.6, "useRowColPositions": false, | ||
| "zNeighborDistance": 0, "excludeCornerNeighbors": false, | ||
| "excludeCompletelyObscuredTiles": false, "excludeSameLayerNeighbors": false, "excludeSameSectionNeighbors": false, | ||
| "excludeSameMfovNeighbors": true, | ||
| "excludePairsInMatchCollection": "pairsFromPriorRuns", "minExistingMatchCount": 0 | ||
| }, | ||
| "matchStageParametersList": [ | ||
| { | ||
| "stageName": "montageMfovPass1", | ||
| "featureExtraction": { "fdSize": 4, "maxScale": 1.0, "minScale": 0.25, "steps": 3 }, | ||
| "featureMatchDerivation": { | ||
| "matchFilter": "SINGLE_SET", "matchFullScaleCoverageRadius": 300.0, "matchIterations": 1000, "matchMaxEpsilonFullScale": 5.0, "matchMaxTrust": 4.0, | ||
| "matchMinCoveragePercentage": 50.0, "matchMinInlierRatio": 0.0, "matchMinNumInliers": 25, "matchModelType": "TRANSLATION", "matchRod": 0.92 | ||
| }, | ||
| "featureRender": { "renderScale": 0.2, "renderWithFilter": true, "renderWithoutMask": false }, | ||
| "featureRenderClip": { "clipHeight": 1300, "clipWidth": 1300 }, | ||
| "geometricDescriptorAndMatch": { "gdEnabled": false } | ||
| }, | ||
| { | ||
| "stageName": "montageMfovPass2", | ||
| "featureExtraction": { "fdSize": 4, "maxScale": 1.0, "minScale": 0.25, "steps": 3 }, | ||
| "featureMatchDerivation": { | ||
| "matchFilter": "SINGLE_SET", "matchFullScaleCoverageRadius": 300.0, "matchIterations": 1000, "matchMaxEpsilonFullScale": 5.0, "matchMaxTrust": 4.0, | ||
| "matchMinCoveragePercentage": 20.0, "matchMinInlierRatio": 0.0, "matchMinNumInliers": 25, "matchModelType": "TRANSLATION", "matchRod": 0.92 | ||
| }, | ||
| "featureRender": { "renderScale": 0.3, "renderWithFilter": true, "renderWithoutMask": false }, | ||
| "featureRenderClip": { "clipHeight": 1300, "clipWidth": 1300 }, | ||
| "geometricDescriptorAndMatch": { "gdEnabled": false } | ||
| }, | ||
| { | ||
| "stageName": "montageMfovPass3", | ||
| "featureExtraction": { "fdSize": 4, "maxScale": 1.0, "minScale": 0.25, "steps": 3 }, | ||
| "featureMatchDerivation": { | ||
| "matchFilter": "SINGLE_SET", "matchFullScaleCoverageRadius": 300.0, "matchIterations": 1000, "matchMaxEpsilonFullScale": 5.0, "matchMaxTrust": 4.0, | ||
| "matchMinCoveragePercentage": 20.0, "matchMinInlierRatio": 0.0, "matchMinNumInliers": 25, "matchModelType": "TRANSLATION", "matchRod": 0.92 | ||
| }, | ||
| "featureRender": { "renderScale": 0.4, "renderWithFilter": true, "renderWithoutMask": false }, | ||
| "featureRenderClip": { "clipHeight": 1300, "clipWidth": 1300 }, | ||
| "geometricDescriptorAndMatch": { "gdEnabled": false } | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "runName": "montageRun", | ||
| "matchCommon": { | ||
| "maxPairsPerStackBatch" : 30, | ||
| "featureStorage": { "maxFeatureSourceCacheGb": 6 }, | ||
| "maxPeakCacheGb" : 2 | ||
| }, | ||
| "tilePairDerivationParameters": { | ||
| "xyNeighborFactor": 0.6, "useRowColPositions": false, | ||
| "zNeighborDistance": 0, "excludeCornerNeighbors": false, | ||
| "excludeCompletelyObscuredTiles": false, "excludeSameLayerNeighbors": false, "excludeSameSectionNeighbors": false, | ||
| "excludePairsInMatchCollection": "pairsFromPriorRuns", "minExistingMatchCount": 0 | ||
| }, | ||
| "matchStageParametersList": [ | ||
| { | ||
| "stageName": "montagePass1", | ||
| "featureExtraction": { "fdSize": 4, "maxScale": 1.0, "minScale": 0.25, "steps": 3 }, | ||
| "featureMatchDerivation": { | ||
| "matchFilter": "SINGLE_SET", "matchFullScaleCoverageRadius": 300.0, "matchIterations": 1000, "matchMaxEpsilonFullScale": 5.0, "matchMaxTrust": 4.0, | ||
| "matchMinCoveragePercentage": 20.0, "matchMinInlierRatio": 0.0, "matchMinNumInliers": 25, "matchModelType": "TRANSLATION", "matchRod": 0.92 | ||
| }, | ||
| "featureRender": { "renderScale": 0.8, "renderWithFilter": true, "renderWithoutMask": false }, | ||
| "featureRenderClip": { "clipHeight": 140, "clipWidth": 80 }, | ||
| "geometricDescriptorAndMatch": { "gdEnabled": false } | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "runName": "crossRun", | ||
| "matchCommon": { | ||
| "maxPairsPerStackBatch" : 50, | ||
| "featureStorage": { "maxFeatureSourceCacheGb": 6 }, | ||
| "maxPeakCacheGb" : 2 | ||
| }, | ||
| "tilePairDerivationParameters": { | ||
| "xyNeighborFactor" : 0.1, "useRowColPositions" : false, | ||
| "zNeighborDistance" : 3, "excludeCornerNeighbors" : false, | ||
| "excludeCompletelyObscuredTiles" : true, "excludeSameLayerNeighbors" : true, "excludeSameSectionNeighbors" : false, | ||
| "excludePairsInMatchCollection": "pairsFromPriorRuns", "minExistingMatchCount": 0 | ||
| }, | ||
| "matchStageParametersList": [ | ||
| { | ||
| "stageName": "crossPass1", | ||
| "featureExtraction": { "fdSize": 4, "maxScale": 1.0, "minScale": 0.125, "steps": 5 }, | ||
| "featureMatchDerivation": { | ||
| "matchFilter": "SINGLE_SET", "matchFullScaleCoverageRadius": 150.0, "matchIterations": 1000, "matchMaxEpsilonFullScale": 5.0, "matchMaxTrust": 4.0, | ||
| "matchMinCoveragePercentage": 50.0, "matchMinInlierRatio": 0.0, "matchMinNumInliers": 40, "matchModelType": "RIGID", "matchRod": 0.92 | ||
| }, | ||
| "featureRender": { "renderScale": 0.14, "renderWithFilter": true, "renderWithoutMask": false }, | ||
| "geometricDescriptorAndMatch": { "gdEnabled": false }, | ||
| "maxNeighborDistance": 3 | ||
| }, | ||
| { | ||
| "stageName": "crossPass2", | ||
| "featureExtraction": { "fdSize": 4, "maxScale": 1.0, "minScale": 0.125, "steps": 5 }, | ||
| "featureMatchDerivation": { | ||
| "matchFilter": "SINGLE_SET", "matchFullScaleCoverageRadius": 150.0, "matchIterations": 1000, "matchMaxEpsilonFullScale": 5.0, "matchMaxTrust": 4.0, | ||
| "matchMinCoveragePercentage": 50.0, "matchMinInlierRatio": 0.0, "matchMinNumInliers": 20, "matchModelType": "RIGID", "matchRod": 0.92 | ||
| }, | ||
| "featureRender": { "renderScale": 0.22, "renderWithFilter": true, "renderWithoutMask": false }, | ||
| "geometricDescriptorAndMatch": { "gdEnabled": false }, | ||
| "maxNeighborDistance": 3 | ||
| }, | ||
| { | ||
| "stageName": "crossPass3", | ||
| "featureExtraction": { "fdSize": 4, "maxScale": 1.0, "minScale": 0.125, "steps": 5 }, | ||
| "featureMatchDerivation": { | ||
| "matchFilter": "AGGREGATED_CONSENSUS_SETS", "matchFullScaleCoverageRadius": 300.0, "matchIterations": 1000, "matchMaxEpsilonFullScale": 5.0, "matchMaxTrust": 4.0, | ||
| "matchMinCoveragePercentage": 0.0, "matchMinInlierRatio": 0.0, "matchMinNumInliers": 10, "matchModelType": "RIGID", "matchRod": 0.92 | ||
| }, | ||
| "featureRender": { "renderScale": 0.4, "renderWithFilter": true, "renderWithoutMask": false }, | ||
| "geometricDescriptorAndMatch": { "gdEnabled": false }, | ||
| "maxNeighborDistance": 1 | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "mfovMontagePatch": { | ||
| "sameLayerDerivedMatchWeight" : 0.15, | ||
| "crossLayerDerivedMatchWeight" : 0.1, | ||
| "secondPassDerivedMatchWeight" : 0.05, | ||
| "xyNeighborFactor" : 0.6, | ||
| "numberOfMFOVsPerBatch": 19 | ||
| }, | ||
| "unconnectedCrossMfov": { | ||
| "minPairsForConnection": 6, | ||
| "numberOfStacksPerBatch": 20 | ||
| } | ||
| } |
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