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tineveztinevez
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Merge pull request #374 from ctrueden/dev
Realign dev branch with latest master branch
2 parents af3aeb5 + ee6fe6f commit 93c8169

10 files changed

Lines changed: 153 additions & 30 deletions

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‎pom.xml‎

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@@ -5,12 +5,12 @@
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<parent>
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<groupId>org.scijava</groupId>
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<artifactId>pom-scijava</artifactId>
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<version>40.0.0</version>
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<version>42.0.0</version>
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</parent>
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<groupId>org.mastodon</groupId>
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<artifactId>mastodon</artifactId>
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<version>1.0.0-beta-35-SNAPSHOT</version>
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<version>1.0.0-beta-36-SNAPSHOT</version>
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<name>Mastodon</name>
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<description>Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.</description>

‎scripts/MastodonScriptExample.py‎

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#@ Context context
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from java.io import File
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from org.mastodon.mamut import WindowManager
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from org.mastodon.mamut.project import MamutProject
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from org.mastodon.tracking.mamut.trackmate import TrackMate
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from org.mastodon.tracking.mamut.trackmate import Settings
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from org.mastodon.tracking.mamut.detection import DoGDetectorMamut
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from org.mastodon.tracking.mamut.linking import SimpleSparseLAPLinkerMamut
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from org.mastodon.tracking.linking import LinkingUtils
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bdv_file = "/Users/tinevez/Development/Mastodon/mastodon/samples/datasethdf5.xml"
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project = MamutProject( None, File( bdv_file ) );
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# Open the project.
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wm = WindowManager( context )
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wm.getProjectManager().open( project )
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app_model = wm.getAppModel()
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# Get Mastodon model.
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model = app_model.getModel()
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selection_model = app_model.getSelectionModel()
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# Get image data.
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image_data = app_model.getSharedBdvData()
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# Configure TrackMate.
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# Detector settings.
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detector_settings = {
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"MIN_TIMEPOINT" : 0,
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"MAX_TIMEPOINT" : 1000,
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"SETUP" : 0, # The channel or source in the BDV data.
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"RADIUS" : 7., # The cell expected radius.
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"THRESHOLD" : 200. # Threshold on quality.
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}
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# Linker settings. There are too many, so we take the default and edit it.
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linker_settings = LinkingUtils.getDefaultLAPSettingsMap()
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linker_settings[ "MIN_TIMEPOINT" ] = 0
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linker_settings[ "MAX_TIMEPOINT" ] = 1000
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linker_settings[ "LINKING_MAX_DISTANCE" ] = 10.
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linker_settings[ "ALLOW_GAP_CLOSING" ] = True
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linker_settings[ "MAX_FRAME_GAP" ] = 2
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# Create the settings objects.
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settings = Settings() \
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.sources( image_data.getSources() ) \
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.detector( DoGDetectorMamut ) \
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.detectorSettings( detector_settings ) \
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.linker( SimpleSparseLAPLinkerMamut ) \
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.linkerSettings( linker_settings )
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trackmate = TrackMate( settings, model, selection_model )
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# We need to give a context to TrackMate.
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trackmate.setContext( context )
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# Run TrackMate.
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trackmate.run()
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if trackmate.isCanceled():
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print( "Calculation was canceled. Reason: " + trackmate.getCancelReason() )
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elif not trackmate.isSuccessful():
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print( "Calculation failed with error message:\n" + trackmate.getErrorMessage() )
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else:
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print( "Calculation complete." );
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wm.createTrackScheme()
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wm.createBigDataViewer()
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# Compute features.
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wm.createTable( False )

‎src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java‎

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/*-
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* #%L
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* Mastodon
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* %%
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* Copyright (C) 2014 - 2025 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.io.importer.trackmate;
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import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_ATTRIBUTE;

‎src/main/java/org/mastodon/mamut/io/loader/util/mobie/OmeZarrMultiscalesAdapter.java‎

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public class OmeZarrMultiscalesAdapter implements JsonDeserializer< OmeZarrMultiscales >, JsonSerializer< OmeZarrMultiscales >
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{
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48-
@SuppressWarnings( "serial" )
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@Override
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public OmeZarrMultiscales deserialize( final JsonElement json, final Type typeOfT, final JsonDeserializationContext context ) throws JsonParseException
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{

‎src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java‎

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import org.janelia.saalfeldlab.n5.metadata.N5ViewerMultichannelMetadata;
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import org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog;
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import org.janelia.saalfeldlab.n5.universe.N5Factory;
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import org.janelia.saalfeldlab.n5.universe.N5Factory.StorageFormat;
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import org.janelia.saalfeldlab.n5.universe.StorageFormat;
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import org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata;
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import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata;
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import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata;
@@ -404,21 +404,14 @@ public N5Reader apply( final String n5UriOrPath )
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String rootPath = null;
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if ( n5UriOrPath.contains( "?" ) )
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{
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try
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{
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// need to strip off storage format for n5uri to correctly
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// remove query;
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final Pair< StorageFormat, URI > fmtUri = N5Factory.StorageFormat.parseUri( n5UriOrPath );
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final StorageFormat format = fmtUri.getA();
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final N5URI n5uri = new N5URI( URI.create( fmtUri.getB().toString() ) );
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// add the format prefix back if it was present
416-
rootPath = format == null ? n5uri.getContainerPath() : format.toString().toLowerCase() + ":" + n5uri.getContainerPath();
417-
}
418-
catch ( final URISyntaxException e )
419-
{
420-
messenger.accept( "The URI is not valid or credentials are missing: " + n5UriOrPath );
421-
}
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// need to strip off storage format for n5uri to correctly
408+
// remove query;
409+
final Pair< StorageFormat, URI > fmtUri = StorageFormat.parseUri( n5UriOrPath );
410+
final StorageFormat format = fmtUri.getA();
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412+
final N5URI n5uri = new N5URI( URI.create( fmtUri.getB().toString() ) );
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// add the format prefix back if it was present
414+
rootPath = format == null ? n5uri.getContainerPath() : format.toString().toLowerCase() + ":" + n5uri.getContainerPath();
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}
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if ( rootPath == null )

‎src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapher.java‎

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import org.mastodon.ui.coloring.GraphColorGeneratorAdapter;
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import org.mastodon.ui.coloring.HasColorBarOverlay;
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import org.mastodon.ui.coloring.HasColoringModel;
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import org.mastodon.ui.commandfinder.CommandFinder;
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import org.mastodon.ui.keymap.KeyConfigContexts;
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import org.mastodon.views.context.ContextChooser;
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import org.mastodon.views.context.HasContextChooser;

‎src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java‎

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return btnPlot;
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}
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278-
public < V, E > void setFeatures(
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public void setFeatures(
279279
final Map< FeatureSpec< ?, V >, Feature< V > > vertexFeatures,
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final Map< FeatureSpec< ?, E >, Feature< E > > edgeFeatures )
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{
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436436
return null;
437437
}
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@Override
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public ContextChooser< V > getContextChooser()
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{
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return this.contextChooser;

‎src/main/java/org/mastodon/views/grapher/display/Plotable.java‎

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/*-
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* #%L
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* Mastodon
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* %%
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* Copyright (C) 2014 - 2025 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
8+
* modification, are permitted provided that the following conditions are met:
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*
10+
* 1. Redistributions of source code must retain the above copyright notice,
11+
* this list of conditions and the following disclaimer.
12+
* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
16+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
18+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
19+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
20+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
21+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
22+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
23+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
24+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
25+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
26+
* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.views.grapher.display;
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import org.mastodon.views.grapher.datagraph.ScreenTransform;

‎src/test/java/org/mastodon/StartMastodonDefaultProject.java‎

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public static void main( final String[] args )
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{
3636
// final String projectPath = "samples/MaMuT_Parhyale_small.mastodon";
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// final String projectPath = "/Users/tinevez/Google Drive/Mastodon/Datasets/Remote/ParhyaleHawaiensis/MaMuT_Parhyale_demo-mamut.mastodon";
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final String projectPath = "samples/drosophila_crop_LONG_NAME_LONGLONGLONG_SUPERLONG.mastodon";
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final String projectPath = "/Users/tinevez/Library/CloudStorage/GoogleDrive-jeanyves.tinevez@gmail.com/My Drive/Mastodon/Datasets/Remote/BDV/Tribolium/CTC_TRIF_trainingVideo02_jy-GT-done.mastodon";
38+
// final String projectPath = "samples/drosophila_crop_LONG_NAME_LONGLONGLONG_SUPERLONG.mastodon";
3939
// final String projectPath = "samples/drosophila_crop.mastodon";
4040
StartMastodonOnProject.launch( projectPath );
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}

‎src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java‎

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import java.io.IOException;
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33-
import org.mastodon.mamut.ProjectModel;
34-
import org.mastodon.mamut.WindowManager;
3533
import org.mastodon.mamut.io.importer.ModelImporter;
3634
import org.mastodon.mamut.io.project.MamutProject;
3735
import org.mastodon.mamut.model.Link;
@@ -184,11 +182,11 @@ public static void main( final String[] args ) throws IOException
184182
( Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory() ) / 1e6d ) );
185183

186184

187-
final Context context = new Context();
188-
final SharedBigDataViewerData imagedata = SharedBigDataViewerData.fromDummyFilename( "x=1000 y=1000 z=100 sx=1 sy=1 sz=10 t=400.dummy" );
189-
final MamutProject project = new MamutProject( "./large_model_example.mastodon" );
190-
final ProjectModel appModel = ProjectModel.create( context, model, imagedata, project );
191-
final WindowManager wm = new WindowManager( appModel );
185+
// final Context context = new Context();
186+
// final SharedBigDataViewerData imagedata = SharedBigDataViewerData.fromDummyFilename( "x=1000 y=1000 z=100 sx=1 sy=1 sz=10 t=400.dummy" );
187+
// final MamutProject project = new MamutProject( "./large_model_example.mastodon" );
188+
// final ProjectModel appModel = ProjectModel.create( context, model, imagedata, project );
189+
// final WindowManager wm = new WindowManager( appModel );
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193191
// start = System.currentTimeMillis();
194192
// wm.createBigDataViewer();

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