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Merge pull request #1064 from mobie/omeZarrHcsS3
Read OME-Zarr HCS from S3
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96 changes: 96 additions & 0 deletions
96
src/main/java/org/embl/mobie/lib/hcs/omezarr/OMEZarrHCSHelper.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| package org.embl.mobie.lib.hcs.omezarr; | ||
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| import com.google.gson.Gson; | ||
| import com.google.gson.reflect.TypeToken; | ||
| import ij.IJ; | ||
| import org.embl.mobie.io.util.IOHelper; | ||
| import org.embl.mobie.lib.MoBIEHelper; | ||
| import org.embl.mobie.lib.ThreadHelper; | ||
| import org.embl.mobie.lib.serialize.JsonHelper; | ||
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| import java.io.IOException; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.concurrent.CopyOnWriteArrayList; | ||
| import java.util.concurrent.Future; | ||
| import java.util.concurrent.atomic.AtomicInteger; | ||
| import java.util.concurrent.atomic.AtomicLong; | ||
| import java.util.stream.Collectors; | ||
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| public class OMEZarrHCSHelper | ||
| { | ||
| public static final String ZATTRS = "/.zattrs"; | ||
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| public static List< String > sitePathsFromFolderStructure( String hcsDirectory ) throws IOException | ||
| { | ||
| List< String > imageSitePaths; | ||
| final int minDepth = 3; | ||
| final int maxDepth = 3; | ||
| final Path rootPath = Paths.get( hcsDirectory ); | ||
| final int rootPathDepth = rootPath.getNameCount(); | ||
| imageSitePaths = Files.walk( rootPath, maxDepth ) | ||
| .filter( e -> e.toFile().isDirectory() ) | ||
| .filter( e -> e.getNameCount() - rootPathDepth >= minDepth ) | ||
| .map( e -> e.toString() ) | ||
| .collect( Collectors.toList() ); | ||
| return imageSitePaths; | ||
| } | ||
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| public static List< String > sitePathsFromMetadata( String hcsDirectory ) throws IOException | ||
| { | ||
| List< String > imageSitePaths = new CopyOnWriteArrayList<>(); | ||
| Gson gson = JsonHelper.buildGson(false); | ||
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| String plateUri = hcsDirectory; | ||
| final String plateJson = IOHelper.read( plateUri + ZATTRS ); | ||
| //System.out.println( plateJson ); | ||
| HCSMetadata hcsMetadata = gson.fromJson(plateJson, new TypeToken< HCSMetadata >() {}.getType()); | ||
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| int numWells = hcsMetadata.plate.wells.size(); | ||
| // lots of code for nice logging... | ||
| AtomicInteger wellIndex = new AtomicInteger(0); | ||
| AtomicInteger sourceLoggingModulo = new AtomicInteger(1); | ||
| AtomicLong lastLogMillis = new AtomicLong( System.currentTimeMillis() ); | ||
| final long startTime = System.currentTimeMillis(); | ||
| IJ.log( "Parsing " + numWells + " wells..." ); | ||
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| ArrayList< Future< ? > > futures = ThreadHelper.getFutures(); | ||
| for ( Well well : hcsMetadata.plate.wells ) | ||
| { | ||
| futures.add( | ||
| ThreadHelper.ioExecutorService.submit( () -> | ||
| { | ||
| String log = MoBIEHelper.getLog( wellIndex, numWells, sourceLoggingModulo, lastLogMillis ); | ||
| if ( log != null ) | ||
| IJ.log( log + well.path ); | ||
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| String wellUri = IOHelper.combinePath( plateUri, well.path); | ||
| final String wellJson; | ||
| try | ||
| { | ||
| wellJson = IOHelper.read( wellUri + ZATTRS ); | ||
| } catch ( IOException e ) | ||
| { | ||
| throw new RuntimeException( e ); | ||
| } | ||
| WellMetadata wellMetadata = gson.fromJson( wellJson, new TypeToken< WellMetadata >() {}.getType() ); | ||
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| for ( Image image : wellMetadata.well.images ) | ||
| { | ||
| String imageUri = IOHelper.combinePath( wellUri, image.path ); | ||
| imageSitePaths.add( imageUri ); | ||
| } | ||
| } | ||
| ) ); | ||
| } | ||
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| ThreadHelper.waitUntilFinished( futures ); | ||
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| IJ.log( "Parsed " + numWells + " wells in " + (System.currentTimeMillis() - startTime) + " ms, using up to " + ThreadHelper.getNumIoThreads() + " thread(s)."); | ||
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| return imageSitePaths; | ||
| } | ||
| } |
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