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Collection table with contrasts per grid position
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| 356acc218258751f5e1ed53ee870d42ab21dd673 20231226200404 README.md | ||
| 2c83491b886d08de395d00c4022aba2a85c71bba 20230807160348 images/74152530-c9603500-4c0e-11ea-81d8-d518b9ed1ef3.png | ||
| 82fdb8b52f6193f76125d9890d321bef40df48c1 20230807160348 images/74152904-98cccb00-4c0f-11ea-9819-6c772174a2c0.png | ||
| a375450e7776d246071f5b50c9f477b8f96eccde 20230807160348 images/74152986-cc0f5a00-4c0f-11ea-869d-23456fec0cdc.png | ||
| bec35cfbf13684d4ef73521e737b7f691492c7f6 20230807160348 images/74168546-37febc00-4c2a-11ea-9981-85232ed5322e.png | ||
| 11f8d83f03952423124d3f46a7a22189fb052190 20230807160348 images/74252332-d2740380-4ced-11ea-9a4e-d25cb1e83859.png | ||
| d238dc37c990bc99d20ed721e1fc7830f999fadc 20230807160348 images/mobie-beta-update-site.png | ||
| 2c4cbd6b245d453691974d4d94d6a95e3a5441a6 20230807160348 images/mobie-logo-highres.png | ||
| 25f4e1de2d22ac36510a496229e4b51d47134f13 20231206194322 scripts/visualise_morpholibj_2d_output.ijm | ||
| 6163a44341132da743ca32573b1b8bed7139b85c 20231206194322 scripts/visualise_morpholibj_3d_output.ijm | ||
| c0b74dc4fb1134303d666aa3e4455c6d54487e05 20231206194322 scripts/visualise_particleanalyzer_2d_output.ijm |
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120 changes: 120 additions & 0 deletions
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src/main/java/org/embl/mobie/command/open/special/OpenMicrogliaTableCommand.java
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| /*- | ||
| * #%L | ||
| * Fiji viewer for MoBIE projects | ||
| * %% | ||
| * Copyright (C) 2018 - 2024 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 org.embl.mobie.command.open.special; | ||
|
|
||
| import loci.common.DebugTools; | ||
| import org.embl.mobie.MoBIE; | ||
| import org.embl.mobie.MoBIESettings; | ||
| import org.embl.mobie.command.CommandConstants; | ||
| import org.embl.mobie.command.SpatialCalibration; | ||
| import org.embl.mobie.lib.MoBIEHelper; | ||
| import org.embl.mobie.lib.transform.GridType; | ||
| import org.scijava.ItemVisibility; | ||
| import org.scijava.command.Command; | ||
| import org.scijava.plugin.Parameter; | ||
| import org.scijava.plugin.Plugin; | ||
|
|
||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| @Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN + "Special>Open Microglia Morphometry Table..." ) | ||
| public class OpenMicrogliaTableCommand implements Command { | ||
|
|
||
| static { net.imagej.patcher.LegacyInjector.preinit(); } | ||
|
|
||
| @Parameter( label = "Table", required = true ) | ||
| public File table; | ||
|
|
||
| @Parameter(visibility = ItemVisibility.MESSAGE, | ||
| persist = false, | ||
| required = false ) | ||
| private String message = "Opens tables created with the Microglia-Morphometry plugin."; | ||
|
|
||
| @Parameter(visibility = ItemVisibility.MESSAGE, | ||
| persist = false, | ||
| required = false) | ||
| private String info = "More info: https://github.com/embl-cba/microglia-morphometry"; | ||
|
|
||
|
|
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| private String images = "Path_Intensities,Path_Skeletons,Path_Annotations"; | ||
|
|
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| private String labels = "Path_LabelMasks"; | ||
|
|
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| private File root; | ||
|
|
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| private String pathMapping; | ||
|
|
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| private SpatialCalibration spatialCalibration = SpatialCalibration.FromImage; | ||
|
|
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| private GridType gridType = GridType.Transformed; | ||
|
|
||
| @Override | ||
| public void run() | ||
| { | ||
| run( gridType ); | ||
| } | ||
|
|
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| private void run( GridType gridType ) | ||
| { | ||
| DebugTools.setRootLevel( "OFF" ); | ||
|
|
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| final MoBIESettings settings = new MoBIESettings(); | ||
|
|
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| spatialCalibration.setVoxelDimensions( settings, table != null ? table.getAbsolutePath() : null ); | ||
| root = table.getParentFile(); | ||
|
|
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| List< String > imageList = new ArrayList<>(); | ||
| if ( images != null && ! images.equals( "" ) ) | ||
| { | ||
| imageList = Arrays.asList( images.split( "," ) ); | ||
| imageList = imageList.stream().map( s -> s.trim() ).collect( Collectors.toList() ); | ||
| } | ||
|
|
||
| List< String > labelList = new ArrayList<>(); | ||
| if ( labels != null && ! labels.equals( "" ) ) | ||
| { | ||
| labelList = Arrays.asList( labels.split( "," ) ); | ||
| labelList = labelList.stream().map( s -> s.trim() ).collect( Collectors.toList() ); | ||
| } | ||
|
|
||
| try | ||
| { | ||
| String rootPath = root == null ? null : root.getAbsolutePath(); | ||
| new MoBIE( table.getAbsolutePath(), imageList, labelList, rootPath, pathMapping ,gridType, settings ); | ||
| } | ||
| catch ( IOException e ) | ||
| { | ||
| e.printStackTrace(); | ||
| } | ||
| } | ||
| } |
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