public void addViewId(int idx, int tp, int angle, int channel, int tile, int illumination) { List< Integer > val = Arrays.asList( new Integer[] {tp, angle, channel, tile, illumination} ); vidToDescription.put( new ViewId(tp, idx), val ); }
public static String createPSFFileName( final ViewId viewId ) { return "psf_t" + viewId.getTimePointId() + "_v" + viewId.getViewSetupId() + ".tif"; } }
final Set< ViewId > newMv = new HashSet<>(); for ( final ViewId view : mv ) newMv.add( new ViewId( view.getTimePointId() + offset, view.getViewSetupId() ) ); final MissingViews newMissingViews = new MissingViews( newMv );
protected ArrayList< Integer > getListOfViewSetupIdsPresentInAllSubsets( final List< Subset< ViewId > > subsets ) { final HashMap< Integer, Integer > viewsetups = new HashMap< Integer, Integer >(); for ( final Subset< ViewId > subset : subsets ) for ( final ViewId viewId : subset.getViews() ) { if ( viewsetups.containsKey( viewId.getViewSetupId() ) ) viewsetups.put( viewId.getViewSetupId(), viewsetups.get( viewId.getViewSetupId() ) + 1 ); else viewsetups.put( viewId.getViewSetupId(), 1 ); } final ArrayList< Integer > setupList = new ArrayList<>(); for ( final int viewSetupId : viewsetups.keySet() ) if ( viewsetups.get( viewSetupId ) == subsets.size() ) setupList.add( viewSetupId ); Collections.sort( setupList ); return setupList; }
@Override public boolean inRange( final V view1, final V view2 ) { // if one of the views is a reference timepoint or if they are from the same timepoint (fixed views are discarded later) if ( view1.getTimePointId() == referenceTimepoint || view2.getTimePointId() == referenceTimepoint || view1.getTimePointId() == view2.getTimePointId() ) return true; else return false; }
if ( lastViewIdCorr == null || !lastViewIdCorr.equals( viewIdCorr ) ) IOFunctions.println( "Removing correspondences in timepointid=" + viewIdCorr.getTimePointId() + ", viewid=" + viewIdCorr.getViewSetupId() ); lastViewIdCorr = viewIdCorr; if ( cc.getDetectionId() == idCorr && cc.getCorrespondingDetectionId() == pair.getDetectionId() && cc.getCorrespondingViewId().equals( vd ) )
@Override public int compare( final Group< V > o1, final Group< V > o2 ) { return Group.getViewsSorted( o1.getViews() ).get( 0 ).compareTo( Group.getViewsSorted( o2.getViews() ).get( 0 ) ); } } );
final GroupedInterestPoint< V > neighborpoint = neighbor.getA(); if ( !neighborpoint.getV().equals( p.getA().getV() )) // do not set false if it is from the same view if ( !neighborpoint.equals( p.getA() ) ) // do not set false if it is the point we searched for neighbor.getB().state = false;
views.add( new ViewId( viewId.getTimePointId(), viewId.getViewSetupId() ) ); for ( final ViewSetup v : viewSetupsToProcess ) final ViewId viewId = new ViewId( t.getId(), v.getId() );
@Override public Dimensions getImageSize( final ViewId view ) { return sb.getImgs().get( view.getViewSetupId() ); }
@Override public boolean inRange( final V view1, final V view2 ) { if ( Math.abs( view2.getTimePointId() - view1.getTimePointId() ) <= maxDistance ) return true; else return false; } }
public ViewLevelId( final ViewId viewId, final int level ) { this.timepointId = viewId.getTimePointId(); this.setupId = viewId.getViewSetupId(); this.level = level; }
@Override public VoxelDimensions getVoxelSize( final ViewId view ) { // if there is no data for the viewId if ( !imageMetaDataCache.containsKey( view ) ) { // check if the data is present for the same viewsetup of another timepoint if ( !viewIdLookUp.containsKey( view.getViewSetupId() ) ) loadMetaData( view ); else return imageMetaDataCache.get( viewIdLookUp.get( view.getViewSetupId() ) ).getB(); } return imageMetaDataCache.get( view ).getB(); }
public static ArrayList< Integer > getAllTimePointsSortedWithoutPresenceCheck( final Collection< ? extends ViewId > vds ) { final HashSet< Integer > timepointSet = new HashSet< Integer >(); for ( final ViewId vd : vds ) timepointSet.add( vd.getTimePointId() ); final ArrayList< Integer > timepoints = new ArrayList< Integer >(); timepoints.addAll( timepointSet ); Collections.sort( timepoints ); return timepoints; }
public static String pvids( final ViewId viewId ) { return viewId.getTimePointId() + "-" + viewId.getViewSetupId(); } @SuppressWarnings("unchecked")
@Override public boolean isPresent( final int t ) { return t >= 0 && t < timePointsOrdered.size() && !missingViews.contains( new ViewId( timePointsOrdered.get( t ).getId(), setupId ) ); }
@Override public Dimensions getImageSize( final ViewId view ) { // if there is no data for the viewId if ( !imageMetaDataCache.containsKey( view ) ) { // check if the data is present for the same viewsetup of another timepoint if ( !viewIdLookUp.containsKey( view.getViewSetupId() ) ) loadMetaData( view ); else return imageMetaDataCache.get( viewIdLookUp.get( view.getViewSetupId() ) ).getA(); } final Pair< Dimensions, VoxelDimensions > dims = imageMetaDataCache.get( view ); return dims == null ? null : dims.getA(); }
public static ArrayList< Integer > getAllTimePointsSortedUnchecked( final Collection< ? extends ViewId > viewIds ) { final HashSet< Integer > timepointSet = new HashSet< Integer >(); for ( final ViewId vd : viewIds ) timepointSet.add( vd.getTimePointId() ); final ArrayList< Integer > timepoints = new ArrayList< Integer >(); timepoints.addAll( timepointSet ); Collections.sort( timepoints ); return timepoints; }
public static String pvid( final ViewId viewId ) { return "tpId=" + viewId.getTimePointId() + " setupId=" + viewId.getViewSetupId(); } public static String pvids( final ViewId viewId ) { return viewId.getTimePointId() + "-" + viewId.getViewSetupId(); }