-
Notifications
You must be signed in to change notification settings - Fork 13
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
11 changed files
with
162 additions
and
116 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
132 changes: 132 additions & 0 deletions
132
src/main/java/org/embl/mobie/command/context/CurrentLocationLoggerCommand.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,132 @@ | ||
| /*- | ||
| * #%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.context; | ||
|
|
||
| import bdv.util.BdvHandle; | ||
| import com.google.gson.Gson; | ||
| import de.embl.cba.bdv.utils.BdvUtils; | ||
| import de.embl.cba.bdv.utils.Logger; | ||
| import net.imglib2.util.LinAlgHelpers; | ||
| import org.embl.mobie.command.CommandConstants; | ||
| import org.embl.mobie.lib.playground.BdvPlaygroundHelper; | ||
| import org.embl.mobie.lib.serialize.JsonHelper; | ||
| import org.embl.mobie.lib.transform.viewer.AffineViewerTransform; | ||
| import org.embl.mobie.lib.transform.viewer.NormalVectorViewerTransform; | ||
| import org.embl.mobie.lib.serialize.transformation.NormalizedAffineViewerTransform; | ||
| import org.embl.mobie.lib.transform.viewer.PositionViewerTransform; | ||
| import net.imglib2.realtransform.AffineTransform3D; | ||
| import org.scijava.plugin.Parameter; | ||
| import org.scijava.plugin.Plugin; | ||
| import sc.fiji.bdvpg.scijava.command.BdvPlaygroundActionCommand; | ||
|
|
||
| @Plugin( type = BdvPlaygroundActionCommand.class, name = CurrentLocationLoggerCommand.NAME, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + CurrentLocationLoggerCommand.NAME ) | ||
| public class CurrentLocationLoggerCommand implements BdvPlaygroundActionCommand | ||
| { | ||
|
|
||
| private static PositionViewerTransform mousePointerPositionTransform; | ||
|
|
||
| static { net.imagej.patcher.LegacyInjector.preinit(); } | ||
|
|
||
| public static final String NAME = "Log Current Location [ C ]"; | ||
|
|
||
| public static final String SHORTCUT = "C"; | ||
|
|
||
| @Parameter | ||
| BdvHandle bdvHandle; | ||
|
|
||
| @Override | ||
| public void run() | ||
| { | ||
| new Thread( () -> | ||
| { | ||
| logCurrentPosition( bdvHandle, | ||
| BdvPlaygroundHelper.getWindowCentreInCalibratedUnits( bdvHandle ), | ||
| null ); | ||
| } ).start(); | ||
| } | ||
|
|
||
| public static void logCurrentPosition( BdvHandle bdvHandle, | ||
| double[] windowCentre, | ||
| double[] mousePointer ) | ||
| { | ||
|
|
||
| // position | ||
| final int timePoint = bdvHandle.getViewerPanel().state().getCurrentTimepoint(); | ||
| final PositionViewerTransform positionViewerTransform = new PositionViewerTransform( windowCentre, timePoint ); | ||
|
|
||
| // affine | ||
| final AffineTransform3D affineTransform3D = new AffineTransform3D(); | ||
| bdvHandle.getViewerPanel().state().getViewerTransform( affineTransform3D ); | ||
| final AffineViewerTransform affineViewerTransform = new AffineViewerTransform( affineTransform3D.getRowPackedCopy(), timePoint ); | ||
|
|
||
| // normalized affine | ||
| final NormalizedAffineViewerTransform normalizedAffineViewerTransform = new NormalizedAffineViewerTransform( bdvHandle ); | ||
|
|
||
| // normal vector | ||
| double[] currentNormalVector = BdvUtils.getCurrentViewNormalVector( bdvHandle ); | ||
| final NormalVectorViewerTransform normalVectorViewerTransform = new NormalVectorViewerTransform( currentNormalVector, timePoint ); | ||
|
|
||
| final Gson gson = JsonHelper.buildGson( false ); | ||
| Logger.log( "" ); | ||
| Logger.log( "# Current location" ); | ||
| Logger.log( "To restore the current location, any of the below {...} JSON strings can be pasted into MoBIE's \"location\" field." ); | ||
| Logger.log( "To share views with other people we recommend using the normalised viewer transform." ); | ||
|
|
||
| Logger.log("## Mouse pointer position" ); | ||
| Double distanceToRecentPosition = null; | ||
| if ( mousePointer == null ) | ||
| { | ||
| Logger.log( "To get this please use the \"" + SHORTCUT + "\" keyboard shortcut to trigger this action." ); | ||
| } | ||
| else | ||
| { | ||
| if ( mousePointerPositionTransform != null ) | ||
| { | ||
| distanceToRecentPosition = LinAlgHelpers.distance( mousePointerPositionTransform.getParameters(), mousePointer ); | ||
| } | ||
| mousePointerPositionTransform = new PositionViewerTransform( mousePointer, timePoint ); | ||
| Logger.log( gson.toJson( mousePointerPositionTransform ) ); | ||
| } | ||
| Logger.log("## Window center position" ); | ||
| Logger.log( gson.toJson( positionViewerTransform ) ); | ||
| Logger.log("## Viewer transform" ); | ||
| Logger.log( gson.toJson( affineViewerTransform ) ); | ||
| Logger.log("## Normalised viewer transform" ); | ||
| Logger.log( gson.toJson( normalizedAffineViewerTransform ) ); | ||
| Logger.log("## Normal vector" ); | ||
| Logger.log( gson.toJson( normalVectorViewerTransform ) ); | ||
|
|
||
| if ( distanceToRecentPosition != null ) | ||
| { | ||
| Logger.log("" ); | ||
| Logger.log( "Distance between current and most recent mouse position: " + distanceToRecentPosition ); | ||
| } | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
96 changes: 0 additions & 96 deletions
96
src/main/java/org/embl/mobie/command/view/CurrentLocationLoggerCommand.java
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.