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Import TrackMate files in Mastodon #345

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merged 4 commits into from
Nov 11, 2024
Merged

Import TrackMate files in Mastodon #345

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b2001d8
Add dimensions required to import TrackMate >v7 files.
tinevez Nov 10, 2024
f713243
Commit a true IJ TIFF for testing.
tinevez Nov 10, 2024
fb271cb
Return a MamutImagePlusProject when importing a TrackMate file.
tinevez Nov 10, 2024
d4203fb
New icons and message for the TrackMate / MaMuT importer.
tinevez Nov 10, 2024
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2 changes: 1 addition & 1 deletion src/main/java/org/mastodon/app/MastodonIcons.java
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ public class MastodonIcons
new ImageIcon( MastodonIcons.class.getResource( "icon-tag-32x32.png" ) );

public static final ImageIcon MAMUT_IMPORT_ICON_MEDIUM =
new ImageIcon( MastodonIcons.class.getResource( "icon-mamut-import-32x32.png" ) );
new ImageIcon( MastodonIcons.class.getResource( "icon-mamut-import-32x32-2.png" ) );

public static final ImageIcon MAMUT_EXPORT_ICON_MEDIUM =
new ImageIcon( MastodonIcons.class.getResource( "icon-mamut-export-32x32.png" ) );
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12 changes: 10 additions & 2 deletions src/main/java/org/mastodon/feature/Dimension.java
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Expand Up @@ -75,7 +75,7 @@ public enum Dimension
*/
TIME( "Time" ),
/**
* Units of angles. We alway pick radians for units.
* Units of angles. We always pick radians for units.
*/
ANGLE( "Angle" ),
/**
Expand All @@ -89,7 +89,11 @@ public enum Dimension
/**
* Non numerical quantities.
*/
STRING( "NA" ); // for non-numeric features
STRING( "NA" ),
/**
* Area.
*/
AREA( "Area" );

public static final String COUNTS_UNITS = "Counts";

Expand Down Expand Up @@ -127,6 +131,8 @@ public String getUnits( final String spaceUnits, final String timeUnits )
{
case ANGLE:
return RADIANS_UNITS;
case ANGLE_RATE:
return RADIANS_UNITS + "/" + timeUnits;
case INTENSITY:
return COUNTS_UNITS;
case INTENSITY_SQUARED:
Expand All @@ -146,6 +152,8 @@ public String getUnits( final String spaceUnits, final String timeUnits )
return spaceUnits + "/" + timeUnits;
case RATE:
return "/" + timeUnits;
case AREA:
return spaceUnits + "²";
default:
case STRING:
return null;
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18 changes: 17 additions & 1 deletion src/main/java/org/mastodon/mamut/io/importer/trackmate/TrackMateImporter.java
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Expand Up @@ -94,6 +94,9 @@
import org.mastodon.properties.DoublePropertyMap;
import org.mastodon.properties.IntPropertyMap;

import ij.IJ;
import ij.ImagePlus;

/**
* Importer for TrackMate (http://imagej.net/TrackMate) files.
* <p>
Expand Down Expand Up @@ -162,7 +165,18 @@ public MamutProject createProject() throws IOException
imageFile = makDummyImage( imageDataEl );
}
}
final MamutProject project = MamutProjectIO.fromBdvFile( imageFile );
final MamutProject project;
if ( imageFile.getAbsolutePath().endsWith( ".xml" ) )
{
// Point to a XML file -> it's a MaMuT file
project = MamutProjectIO.fromBdvFile( imageFile );
}
else
{
// Everything else: we assume it's an IJ image.
final ImagePlus imp = IJ.openImage( imageFile.getAbsolutePath() );
project = MamutProjectIO.fromImagePlus( imp );
}

// Set project time and space units
final Element modelEl = root.getChild( MODEL_TAG );
Expand Down Expand Up @@ -523,6 +537,8 @@ private static final Dimension dimensionToDimension( final String dimension )
return Dimension.COST;
case "ANGLE_RATE":
return Dimension.ANGLE_RATE;
case "AREA":
return Dimension.AREA;

default:
throw new IllegalArgumentException( "Unkown dimension " + dimension );
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2 changes: 1 addition & 1 deletion src/main/java/org/mastodon/mamut/launcher/LauncherGUI.java
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Expand Up @@ -180,7 +180,7 @@ public LauncherGUI( final Consumer< String > projectOpener )
sidePanel.add( btnImportMamut, c );

c.gridx = 1;
sidePanel.add( new JLabel( "import MaMuT" ), c );
sidePanel.add( new JLabel( "<html>import TrackMate<br>&amp; MaMuT</html>" ), c );

c.gridx = 0;
c.gridy++;
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Binary file added src/main/resources/org/mastodon/app/icon-mamut-import-16x16-2.png
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Binary file added src/main/resources/org/mastodon/app/icon-mamut-import-32x32-2.png
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Binary file added src/main/resources/org/mastodon/app/icon-mamut-import-512x512-2.png
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Binary file modified src/test/resources/org/mastodon/mamut/io/importer/FakeTracks.tif
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