public static TimePoints createTimepoints() { final ArrayList< TimePoint > timepointList = new ArrayList< TimePoint >(); timepointList.add( new TimePoint( 0 ) ); return new TimePoints( timepointList ); }
protected static TimePoints createTimePoints( final SPIMConfiguration conf ) { final ArrayList< TimePoint > timepoints = new ArrayList<>(); for ( final int tp : conf.timepoints ) timepoints.add( new TimePoint( tp ) ); return new TimePoints( timepoints ); }
public static TimePoints createTimePointsFromImgLoader(SimulatedBeadsImgLoader2 imgLoader) { final ArrayList< TimePoint > timepointList = new ArrayList< TimePoint >(); SimulateBeads2 sb = imgLoader.getSimulateBeads(); for (int tp : new ArrayList<>(sb.tpTransforms.keySet()).stream().sorted().collect( Collectors.toList() )) timepointList.add( new TimePoint( tp ) ); return new TimePoints( timepointList ); }
protected TimePoints createTimePoints( final LightSheetZ1MetaData meta ) { final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >(); for ( int t = 0; t < meta.numTimepoints(); ++t ) timepoints.add( new TimePoint( t ) ); return new TimePoints( timepoints ); }
static LoopBackImageLoader create( final IHDF5Reader existingHdf5Reader, final int timepointIdPartition, final int setupIdPartition, final Dimensions imageDimensions ) { final HashMap< Integer, TimePoint > timepoints = new HashMap<>(); timepoints.put( timepointIdPartition, new TimePoint( timepointIdPartition ) ); final HashMap< Integer, BasicViewSetup > setups = new HashMap<>(); setups.put( setupIdPartition, new BasicViewSetup( setupIdPartition, null, imageDimensions, null ) ); final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups, null, null ); return new LoopBackImageLoader( existingHdf5Reader, seq ); } }
protected TimePoints createTimePoints( MultipageTiffReader meta ) { final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >(); for ( int t = 0; t < meta.numTimepoints(); ++t ) timepoints.add( new TimePoint( t ) ); return new TimePoints( timepoints ); }
protected TimePoints createTimePoints( final DHMMetaData meta ) { final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >(); for ( int t = 0; t < meta.getTimepoints().size(); ++t ) timepoints.add( new TimePoint( Integer.parseInt( meta.getTimepoints().get( t ) ) ) ); return new TimePoints( timepoints ); }
public TimePoints readTimePoints() { final Element root = document.getRootElement(); final int nTimePoints = Integer.parseInt( root.getChild( "TimelapsCondition" ).getChildText( "Iteration" ) ); final List< TimePoint > timepoints = new ArrayList<>( nTimePoints ); for ( int i = 0; i < nTimePoints; i++ ) { timepoints.add( new TimePoint( Integer.valueOf( i ) ) ); } return new TimePoints( timepoints ); }
public static void main( String args[] ) { final ArrayList< RegistrationStatistics > data = defaultData(); final ArrayList< TimePoint > tps = new ArrayList< TimePoint >(); for ( final RegistrationStatistics rs : data ) tps.add( new TimePoint( rs.getTimePoint() ) ); final ArrayList< SelectTimepointEntry > items = new ArrayList< SelectTimepointEntry >(); //items.add( new SelectTimepointEntry( "Select Timepoint", data ) ); plotData( new TimePoints( tps ), data, getOptimalTimePoint( data ), true, items ); }
private static TimePoints createTimepointsFromXml( final Element sequenceDescription ) { final Element timepoints = sequenceDescription.getChild( "Timepoints" ); final String type = timepoints.getAttributeValue( "type" ); if ( type.equals( "range" ) ) { final int first = Integer.parseInt( timepoints.getChildText( "first" ) ); final int last = Integer.parseInt( timepoints.getChildText( "last" ) ); final ArrayList< TimePoint > tps = new ArrayList<>(); for ( int i = first, t = 0; i <= last; ++i, ++t ) tps.add( new TimePoint( t ) ); return new TimePoints( tps ); } else { throw new RuntimeException( "unknown <Timepoints> type: " + type ); } }
final SequenceDescription sequenceDescription = new SequenceDescription( new TimePoints( timepoints ), viewSetups, null, missingViews ); final ImgLoader imgLoader = new MicroManagerImgLoader( mmFile, sequenceDescription ); sequenceDescription.setImgLoader( imgLoader );
SequenceDescription sd = new SequenceDescription( new TimePoints( timePoints ), viewSetups , null, new MissingViews( missingViewIds ));
final SequenceDescription seq = new SequenceDescription( new TimePoints( newTimepoints ), newViewSetups, null, null );
tps.put( tpReassigned.getId(), tpReassigned ); final TimePoints newTps = new TimePoints( tps );
final SequenceDescription sequenceDescription = new SequenceDescription( new TimePoints( timepoints ), viewSetups, null, new MissingViews( new ArrayList<>() ) );
aggregateTpIds.putAll( tps ); TimePoints aggregateTimepoints = new TimePoints( aggregateTpIds ); for ( final SpimDataMinimal spimData : spimDatas )
final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepointMap ), setupMap, null, null ); @SuppressWarnings( { "rawtypes", "unchecked" } ) // TODO: when ij2 supports java 7, replace SuppressWarnings by new ImarisImageLoader<>(...) final ImarisImageLoader<?,?,?> imgLoader = new ImarisImageLoader( dataType, new File( fn ), mipmapInfo, dimensions, seq );
final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepointsToCrop ), cropSetups, cropper, null );
for ( int t = 0; t < numTimepoints; ++t ) timepoints.add( new TimePoint( t ) ); final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups, imgLoader, null );
for ( int t = 0; t < numTimepoints; ++t ) timepoints.add( new TimePoint( t ) ); final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups, imgLoader, null );