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66
src/main/java/org/embl/mobie/lib/hcs/omezarr/OMEZarrHCSHelper.java
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| @@ -0,0 +1,66 @@ | ||
| package org.embl.mobie.lib.hcs.omezarr; | ||
|
|
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| import com.google.gson.Gson; | ||
| import com.google.gson.reflect.TypeToken; | ||
| import org.embl.mobie.io.util.IOHelper; | ||
| import org.embl.mobie.lib.serialize.JsonHelper; | ||
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|
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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.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 ArrayList<>(); | ||
| 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 i = 0; | ||
| for ( Well well : hcsMetadata.plate.wells ) | ||
| { | ||
| System.out.println( "Parsing well: " + well.path ); | ||
| String wellPath = well.path; | ||
| String wellUri = IOHelper.combinePath( plateUri, wellPath); | ||
| final String wellJson = IOHelper.read( wellUri + ZATTRS ); | ||
| 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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| i++; | ||
| if ( i > 1 ) break; | ||
| } | ||
|
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| return imageSitePaths; | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,46 @@ | ||
| /*- | ||
| * #%L | ||
| * Fiji viewer for MoBIE projects | ||
| * %% | ||
| * Copyright (C) 2018 - 2023 EMBL | ||
| * %% | ||
| * Redistribution and use in source and binary forms, with or without | ||
| * modification, are permitted provided that the following conditions are met: | ||
| * | ||
| * 1. Redistributions of source code must retain the above copyright notice, | ||
| * this list of conditions and the following disclaimer. | ||
| * 2. Redistributions in binary form must reproduce the above copyright notice, | ||
| * this list of conditions and the following disclaimer in the documentation | ||
| * and/or other materials provided with the distribution. | ||
| * | ||
| * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
| * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE | ||
| * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | ||
| * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF | ||
| * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS | ||
| * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN | ||
| * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) | ||
| * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE | ||
| * POSSIBILITY OF SUCH DAMAGE. | ||
| * #L% | ||
| */ | ||
| package hcs; | ||
|
|
||
| import mpicbg.spim.data.SpimDataException; | ||
| import net.imagej.ImageJ; | ||
| import org.embl.mobie.MoBIE; | ||
| import org.embl.mobie.MoBIESettings; | ||
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| import java.io.IOException; | ||
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| class HCSOMEZarrS3 | ||
| { | ||
| public static void main( String[] args ) throws SpimDataException, IOException | ||
| { | ||
| new ImageJ().ui().showUI(); | ||
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| new MoBIE( "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/plates/5966.zarr", new MoBIESettings(), 0.1, 0.0 ); | ||
| } | ||
| } |