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Minor tweak to the N5 UI.
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- centered in the screen
- disabled after clicking ok
- 'create' button is disabled unless we successfully created a
BDV file
- info log is cleared when a new dataset is queries, or when
canceling.
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@tinevez
tinevez committed Oct 10, 2024
1 parent a8bd714 commit d88b83e
Showing 1 changed file with 158 additions and 144 deletions.
302 changes: 158 additions & 144 deletions src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,7 @@
import org.mastodon.mamut.io.loader.N5UniverseImgLoader;
import org.mastodon.mamut.io.loader.util.credentials.AWSCredentialsManager;
import org.mastodon.mamut.io.loader.util.credentials.AWSCredentialsTools;
import org.mastodon.ui.util.EverythingDisablerAndReenabler;

import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
Expand Down Expand Up @@ -142,149 +143,7 @@ public NewFromUrlPanel( final String panelTitle, final String buttonTitle )
/*
* Wire listeners.
*/
btnBrowse.addActionListener( l -> {
xmlFile = null;
final ExecutorService exec = Executors.newFixedThreadPool( ij.Prefs.getThreads() );
final DatasetSelectorDialog dialog = new DatasetSelectorDialog(
new N5ViewerReaderFun(),
new N5Importer.N5BasePathFun(),
lastOpenedContainer,
N5ViewerCreator.n5vGroupParsers,
N5ViewerCreator.n5vParsers );

dialog.setLoaderExecutor( exec );
dialog.setContainerPathUpdateCallback( x -> lastOpenedContainer = x );
dialog.setTreeRenderer( new N5ViewerTreeCellRenderer( false ) );

dialog.run( selection -> {
N5Metadata metadata = selection.metadata.get( 0 );
long[] dimensions = null;
double[] scales = null;
String[] axisLabels = null;
String unit = null;
AffineTransform3D calib = null;
int x = 1;
int y = 1;
int z = 1;
int c = 1;
int t = 1;
double sx = 1.0;
double sy = 1.0;
double sz = 1.0;
if ( metadata instanceof OmeNgffMetadata )
{
final NgffSingleScaleAxesMetadata setup0Level0Metadata =
( ( OmeNgffMetadata ) metadata ).multiscales[ 0 ].getChildrenMetadata()[ 0 ];
dimensions = setup0Level0Metadata.getAttributes().getDimensions();
scales = setup0Level0Metadata.getScale();
axisLabels = setup0Level0Metadata.getAxisLabels();
unit = setup0Level0Metadata.unit();
if ( unit == null || unit.isEmpty() )
unit = "pixel";
calib = setup0Level0Metadata.spatialTransform3d();
}
else if ( metadata instanceof N5ViewerMultichannelMetadata )
{
c = ( ( N5ViewerMultichannelMetadata ) metadata ).getChildrenMetadata().length;
final MultiscaleMetadata< ? > setup0Metadata =
( ( N5ViewerMultichannelMetadata ) metadata ).getChildrenMetadata()[ 0 ];
final N5SingleScaleMetadata setup0Level0Metadata = ( N5SingleScaleMetadata ) setup0Metadata.getChildrenMetadata()[ 0 ];
dimensions = setup0Level0Metadata.getAttributes().getDimensions();
scales = setup0Level0Metadata.getPixelResolution();
final DefaultAxisMetadata axes = AxisUtils.defaultN5ViewerAxes( ( setup0Level0Metadata ) );
axisLabels = axes.getAxisLabels();
unit = setup0Level0Metadata.unit();
if ( unit == null || unit.isEmpty() )
unit = "pixel";
calib = setup0Level0Metadata.spatialTransform3d();
}
else
{
SwingUtilities.invokeLater(
() -> IJ.error( "Metadata not supported", "The metadata is not supported: " + metadata.getName() ) );
return;
}
final AffineTransform3D calibFinal = calib.copy();

for ( int i = 0; i < axisLabels.length; i++ )
{
if ( axisLabels[ i ].toLowerCase().equals( "x" ) )
{
x = ( int ) dimensions[ i ];
sx = scales[ i ];
}
else if ( axisLabels[ i ].toLowerCase().equals( "y" ) )
{
y = ( int ) dimensions[ i ];
sy = scales[ i ];
}
else if ( axisLabels[ i ].toLowerCase().equals( "z" ) )
{
z = ( int ) dimensions[ i ];
sz = scales[ i ];
}
else if ( axisLabels[ i ].toLowerCase().equals( "c" ) )
c = ( int ) dimensions[ i ];
else if ( axisLabels[ i ].toLowerCase().equals( "t" ) )
t = ( int ) dimensions[ i ];
}
final Dimensions imageSize = new FinalDimensions( x, y, z );
final TimePoints timepoints = new TimePoints(
IntStream.range( 0, t ).mapToObj( TimePoint::new ).collect( Collectors.toList() ) );
final Map< Integer, BasicViewSetup > setups = new HashMap<>();
final VoxelDimensions voxelDimensions = new FinalVoxelDimensions( unit, sx, sy, sz );
for ( int i = 0; i < c; i++ )
setups.put( i, new BasicViewSetup( i, String.format( "channel %d", i ), imageSize, voxelDimensions ) );
final BasicImgLoader imgLoader =
new N5UniverseImgLoader( selection.n5.getURI().toString(), metadata.getPath(), null );
final SequenceDescriptionMinimal sequenceDescription =
new SequenceDescriptionMinimal( timepoints, setups, imgLoader, null );
final ViewRegistrations viewRegistrations = new ViewRegistrations(
IntStream.range( 0, t )
.boxed()
.flatMap( tp -> IntStream.range( 0, setups.size() )
.mapToObj( setup -> new ViewRegistration( tp, setup, calibFinal ) ) )
.collect( Collectors.toList() )
);

final JFileChooser fileChooser = new JFileChooser();
fileChooser.setDialogTitle( "Save BigDataViewer XML File" );
final FileNameExtensionFilter xmlFilter = new FileNameExtensionFilter( "XML Files", "xml" );
fileChooser.setFileFilter( xmlFilter );
final String currDir = IJ.getDirectory( "current" );
if ( currDir != null )
fileChooser.setCurrentDirectory( new File( currDir ) );
int userSelection = fileChooser.showSaveDialog( null );
if ( userSelection == JFileChooser.APPROVE_OPTION )
{
File fileToSave = fileChooser.getSelectedFile();

// Ensure the file has the .xml extension
if ( !fileToSave.getAbsolutePath().endsWith( ".xml" ) )
{
fileToSave = new File( fileToSave.getAbsolutePath() + ".xml" );
}

final SpimDataMinimal spimData =
new SpimDataMinimal( fileToSave.getParentFile(), sequenceDescription, viewRegistrations );

try
{
new XmlIoSpimDataMinimal().save( spimData, fileToSave.getAbsolutePath() );
}
catch ( SpimDataException e )
{
e.printStackTrace();
}

if ( checkBDVFile( fileToSave ) )
{
xmlFile = fileToSave;
}

}
} );
} );
btnBrowse.addActionListener( e -> openBrowserWindow() );

labelInfo = new JLabel( "" );
final GridBagConstraints gbcLabelInfo = new GridBagConstraints();
Expand All @@ -295,13 +154,167 @@ else if ( axisLabels[ i ].toLowerCase().equals( "t" ) )
add( labelInfo, gbcLabelInfo );

btnCreate = new JButton( buttonTitle );
btnCreate.setEnabled( false );
final GridBagConstraints gbcBtnCreate = new GridBagConstraints();
gbcBtnCreate.anchor = GridBagConstraints.EAST;
gbcBtnCreate.gridx = 0;
gbcBtnCreate.gridy = row++;
add( btnCreate, gbcBtnCreate );
}

private void openBrowserWindow()
{
xmlFile = null;
final ExecutorService exec = Executors.newFixedThreadPool( ij.Prefs.getThreads() );
final DatasetSelectorDialog dialog = new DatasetSelectorDialog(
new N5ViewerReaderFun(),
new N5Importer.N5BasePathFun(),
lastOpenedContainer,
N5ViewerCreator.n5vGroupParsers,
N5ViewerCreator.n5vParsers );

dialog.setLoaderExecutor( exec );
dialog.setContainerPathUpdateCallback( x -> lastOpenedContainer = x );
dialog.setTreeRenderer( new N5ViewerTreeCellRenderer( false ) );

btnCreate.setEnabled( false );
labelInfo.setText( "" );

dialog.run( selection -> {

// Disable UI when clicking ok.
final EverythingDisablerAndReenabler disabler = new EverythingDisablerAndReenabler( SwingUtilities.getWindowAncestor( dialog.getJTree() ), null );
disabler.disable();

final N5Metadata metadata = selection.metadata.get( 0 );
long[] dimensions = null;
double[] scales = null;
String[] axisLabels = null;
String unit = null;
AffineTransform3D calib = null;
int x = 1;
int y = 1;
int z = 1;
int c = 1;
int t = 1;
double sx = 1.0;
double sy = 1.0;
double sz = 1.0;
if ( metadata instanceof OmeNgffMetadata )
{
final NgffSingleScaleAxesMetadata setup0Level0Metadata =
( ( OmeNgffMetadata ) metadata ).multiscales[ 0 ].getChildrenMetadata()[ 0 ];
dimensions = setup0Level0Metadata.getAttributes().getDimensions();
scales = setup0Level0Metadata.getScale();
axisLabels = setup0Level0Metadata.getAxisLabels();
unit = setup0Level0Metadata.unit();
if ( unit == null || unit.isEmpty() )
unit = "pixel";
calib = setup0Level0Metadata.spatialTransform3d();
}
else if ( metadata instanceof N5ViewerMultichannelMetadata )
{
c = ( ( N5ViewerMultichannelMetadata ) metadata ).getChildrenMetadata().length;
final MultiscaleMetadata< ? > setup0Metadata =
( ( N5ViewerMultichannelMetadata ) metadata ).getChildrenMetadata()[ 0 ];
final N5SingleScaleMetadata setup0Level0Metadata = ( N5SingleScaleMetadata ) setup0Metadata.getChildrenMetadata()[ 0 ];
dimensions = setup0Level0Metadata.getAttributes().getDimensions();
scales = setup0Level0Metadata.getPixelResolution();
final DefaultAxisMetadata axes = AxisUtils.defaultN5ViewerAxes( ( setup0Level0Metadata ) );
axisLabels = axes.getAxisLabels();
unit = setup0Level0Metadata.unit();
if ( unit == null || unit.isEmpty() )
unit = "pixel";
calib = setup0Level0Metadata.spatialTransform3d();
}
else
{
SwingUtilities.invokeLater(
() -> IJ.error( "Metadata not supported", "The metadata is not supported: " + metadata.getName() ) );
return;
}
final AffineTransform3D calibFinal = calib.copy();

for ( int i = 0; i < axisLabels.length; i++ )
{
if ( axisLabels[ i ].toLowerCase().equals( "x" ) )
{
x = ( int ) dimensions[ i ];
sx = scales[ i ];
}
else if ( axisLabels[ i ].toLowerCase().equals( "y" ) )
{
y = ( int ) dimensions[ i ];
sy = scales[ i ];
}
else if ( axisLabels[ i ].toLowerCase().equals( "z" ) )
{
z = ( int ) dimensions[ i ];
sz = scales[ i ];
}
else if ( axisLabels[ i ].toLowerCase().equals( "c" ) )
c = ( int ) dimensions[ i ];
else if ( axisLabels[ i ].toLowerCase().equals( "t" ) )
t = ( int ) dimensions[ i ];
}
final Dimensions imageSize = new FinalDimensions( x, y, z );
final TimePoints timepoints = new TimePoints(
IntStream.range( 0, t ).mapToObj( TimePoint::new ).collect( Collectors.toList() ) );
final Map< Integer, BasicViewSetup > setups = new HashMap<>();
final VoxelDimensions voxelDimensions = new FinalVoxelDimensions( unit, sx, sy, sz );
for ( int i = 0; i < c; i++ )
setups.put( i, new BasicViewSetup( i, String.format( "channel %d", i ), imageSize, voxelDimensions ) );
final BasicImgLoader imgLoader =
new N5UniverseImgLoader( selection.n5.getURI().toString(), metadata.getPath(), null );
final SequenceDescriptionMinimal sequenceDescription =
new SequenceDescriptionMinimal( timepoints, setups, imgLoader, null );
final ViewRegistrations viewRegistrations = new ViewRegistrations(
IntStream.range( 0, t )
.boxed()
.flatMap( tp -> IntStream.range( 0, setups.size() )
.mapToObj( setup -> new ViewRegistration( tp, setup, calibFinal ) ) )
.collect( Collectors.toList() ) );

final JFileChooser fileChooser = new JFileChooser();
fileChooser.setDialogTitle( "Save BigDataViewer XML File" );
final FileNameExtensionFilter xmlFilter = new FileNameExtensionFilter( "XML Files", "xml" );
fileChooser.setFileFilter( xmlFilter );
final String currDir = IJ.getDirectory( "current" );
if ( currDir != null )
fileChooser.setCurrentDirectory( new File( currDir ) );
final int userSelection = fileChooser.showSaveDialog( null );
if ( userSelection == JFileChooser.APPROVE_OPTION )
{
File fileToSave = fileChooser.getSelectedFile();

// Ensure the file has the .xml extension
if ( !fileToSave.getAbsolutePath().endsWith( ".xml" ) )
{
fileToSave = new File( fileToSave.getAbsolutePath() + ".xml" );
}

final SpimDataMinimal spimData =
new SpimDataMinimal( fileToSave.getParentFile(), sequenceDescription, viewRegistrations );

try
{
new XmlIoSpimDataMinimal().save( spimData, fileToSave.getAbsolutePath() );
}
catch ( final SpimDataException e )
{
e.printStackTrace();
}

if ( checkBDVFile( fileToSave ) )
{
xmlFile = fileToSave;
btnCreate.setEnabled( true );
}
}
} );
SwingUtilities.getWindowAncestor( dialog.getJTree() ).setLocationRelativeTo( this );
}

boolean checkBDVFile( final File file )
{
try
Expand Down Expand Up @@ -334,7 +347,8 @@ public N5Reader apply( final String n5UriOrPath )
{
try
{
// need to strip off storage format for n5uri to correctly remove query;
// need to strip off storage format for n5uri to correctly
// remove query;
final Pair< StorageFormat, URI > fmtUri = N5Factory.StorageFormat.parseUri( n5UriOrPath );
final StorageFormat format = fmtUri.getA();

Expand Down

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