How to use

getId

method

in

mpicbg.spim.data.sequence.Channel

public static ArrayList< ViewDescription > getAllViewIdsForChannelSorted( final SpimData data, final Collection< ? extends ViewId > viewIds, final Channel channel )
{
  final ArrayList< ViewDescription > views = new ArrayList< ViewDescription >();
  for ( final ViewId id : viewIds )
  {
    final ViewDescription vd = data.getSequenceDescription().getViewDescription( id );
    
    if ( vd.isPresent() && vd.getViewSetup().getChannel().getId() == channel.getId() )
      views.add( vd );
  }
  Collections.sort( views );
  return views;
}

  @Override
  public int compare( final ViewId o1, final ViewId o2 )
  {
    final int id1 = sd.getViewDescriptions().get( o1 ).getViewSetup().getAttribute( Channel.class ).getId();
    final int id2 = sd.getViewDescriptions().get( o2 ).getViewSetup().getAttribute( Channel.class ).getId();
    return id1 - id2;
  }
} );

public static ArrayList< ViewDescription > getAllViewIdsForChannelTimePointSorted( final SpimData data, final Collection< ? extends ViewId > viewIds, final Channel channel, final TimePoint timePoint )
{
  final ArrayList< ViewDescription > views = new ArrayList< ViewDescription >();
  for ( final ViewId id : viewIds )
  {
    final ViewDescription vd = data.getSequenceDescription().getViewDescription( id );
    
    if ( vd.isPresent() && vd.getViewSetup().getChannel().getId() == channel.getId() && id.getTimePointId() == timePoint.getId() )
      views.add( vd );
  }
  Collections.sort( views );
  return views;
}

final Channel c2 = vd2.getViewSetup().getChannel();
if ( c1.getId() == cA.getId() && c2.getId() == cB.getId() || c1.getId() == cB.getId() && c2.getId() == cA.getId() )

public static ArrayList< Angle > getAllAnglesForChannelTimepointSorted( final SpimData data, final Collection< ? extends ViewId > viewIds, final Channel c, final TimePoint t )
{
  final HashSet< Angle > angleSet = new HashSet< Angle >();
  for ( final ViewId v : viewIds )
  {
    final ViewDescription vd = data.getSequenceDescription().getViewDescription( v );
    
    if ( vd.isPresent() && v.getTimePointId() == t.getId() && vd.getViewSetup().getChannel().getId() == c.getId() )
      angleSet.add( vd.getViewSetup().getAngle() );
  }
  final ArrayList< Angle > angles = new ArrayList< Angle >();
  angles.addAll( angleSet );
  Collections.sort( angles );
  return angles;
}

public static ArrayList< Illumination > getAllIlluminationsForChannelTimepointSorted( final SpimData data, final Collection< ? extends ViewId > viewIds, final Channel c, final TimePoint t )
{
  final HashSet< Illumination > illumSet = new HashSet< Illumination >();
  for ( final ViewId v : viewIds )
  {
    final ViewDescription vd = data.getSequenceDescription().getViewDescription( v );
    
    if ( vd.isPresent() && v.getTimePointId() == t.getId() && vd.getViewSetup().getChannel().getId() == c.getId() )
      illumSet.add( vd.getViewSetup().getIllumination() );
  }
  final ArrayList< Illumination > illums = new ArrayList< Illumination >();
  illums.addAll( illumSet );
  Collections.sort( illums );
  return illums;
}

  @Override
  public int compare( final ViewId o1, final ViewId o2 )
  {
    return sd.getViewDescription( o1 ).getViewSetup().getChannel().getId() - sd.getViewDescription( o2 ).getViewSetup().getChannel().getId();
  }
} );

  t.setLocation( locations.get( new ViewSetupPrecursor( c.getId(), i.getId(), a.getId(), t.getId() ) ) );
final Calibration cal = calibrations.get( new ViewSetupPrecursor( c.getId(), i.getId(), a.getId(), t.getId() ) );
final VoxelDimensions voxelSize = new FinalVoxelDimensions( cal.calUnit, cal.calX, cal.calY, cal.calZ );

public static FusionResult create(
    final SpimRegistrationSequence spimseq,
    final String filepath,
    final String filepattern,
    final int numSlices,
    final double sliceValueMin,
    final double sliceValueMax,
    final Map< Integer, AffineTransform3D > perTimePointFusionTransforms )
{
  // add one fused ViewSetup per channel in the SpimRegistrationSequence
  final List< Integer > channels = new ArrayList<>();
  for ( final BasicViewSetup setup : spimseq.getSequenceDescription().getViewSetupsOrdered() )
  {
    final int channel = setup.getAttribute( Channel.class ).getId();
    if ( ! channels.contains( channel ) )
      channels.add( channel );
  }
  final TimePoints timepoints = spimseq.getSequenceDescription().getTimePoints();
  return new FusionResult( filepath, filepattern, channels, timepoints, numSlices, sliceValueMin, sliceValueMax, perTimePointFusionTransforms );
}

public static String getTitle( final int splittingType, final Group< ViewDescription > group )
{
  String title;
  final ViewDescription vd0 = group.iterator().next();
  if ( splittingType == 0 ) // "Each timepoint & channel"
    title = "fused_tp_" + vd0.getTimePointId() + "_ch_" + vd0.getViewSetup().getChannel().getId();
  else if ( splittingType == 1 ) // "Each timepoint, channel & illumination"
    title = "fused_tp_" + vd0.getTimePointId() + "_ch_" + vd0.getViewSetup().getChannel().getId() + "_illum_" + vd0.getViewSetup().getIllumination().getId();
  else if ( splittingType == 2 ) // "All views together"
    title = "fused";
  else // "All views"
    title = "fused_tp_" + vd0.getTimePointId() + "_vs_" + vd0.getViewSetupId();
  return title;
}

public static ViewSetup getViewSetup( final List< ? extends ViewSetup > list, final Channel c, final Angle a, final Illumination i, final Tile x )
{
  for ( final ViewSetup viewSetup : list )
  {
    if ( viewSetup.getAngle().getId() == a.getId() && 
       viewSetup.getChannel().getId() == c.getId() && 
       viewSetup.getIllumination().getId() == i.getId() &&
       viewSetup.getTile().getId() == x.getId() )
    {
      return viewSetup;
    }
  }
  return null;
}

public static final ArrayList< ViewDescription > assembleInputData(
    final SpimData2 spimData,
    final TimePoint timepoint,
    final Channel channel,
    final List< ViewId > viewIdsToProcess )
{
  final ArrayList< ViewDescription > inputData = new ArrayList< ViewDescription >();
  for ( final ViewId viewId : viewIdsToProcess )
  {
    final ViewDescription vd = spimData.getSequenceDescription().getViewDescription(
        viewId.getTimePointId(), viewId.getViewSetupId() );
    if ( !vd.isPresent() || vd.getTimePointId() != timepoint.getId() || vd.getViewSetup().getChannel().getId() != channel.getId() )
      continue;
    // get the most recent model
    spimData.getViewRegistrations().getViewRegistration( viewId ).updateModel();
    inputData.add( vd );
  }
  return inputData;
}

/**
 * find ViewSetup index corresponding to given (angle, illumination,
 * channel) triple.
 *
 * @return setup index or -1 if no corresponding setup was found.
 */
protected static int getViewSetupId( final ArrayList< ViewSetup > setups, final int angle, final int illumination, final int channel )
{
  for ( final ViewSetup s : setups )
    if ( s.getAngle().getId() == angle && s.getIllumination().getId() == illumination && s.getChannel().getId() == channel )
      return s.getId();
  return -1;
}

@Override
public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
{
  final BasicViewDescription< ? > vd = sd.getViewDescriptions().get( view );
  final Dimensions d = vd.getViewSetup().getSize();
  final VoxelDimensions dv = vd.getViewSetup().getVoxelSize();
  final ArrayImg< FloatType, ? > img = ArrayImgs.floats( d.dimension( 0 ), d.dimension( 1 ), d.dimension(  2 ) );
  final String ampOrPhaseDir;
  if ( vd.getViewSetup().getAttribute( Channel.class ).getId() == ampChannelId )
    ampOrPhaseDir = amplitudeDir;
  else if ( vd.getViewSetup().getAttribute( Channel.class ).getId() ==  phaseChannelId )
    ampOrPhaseDir = phaseDir;
  else
    throw new RuntimeException( "viewSetupId=" + view.getViewSetupId() + " is not Amplitude nor phase." );
  populateImage( img, directory, stackDir, ampOrPhaseDir, zPlanes, timepoints.get( view.getTimePointId() ), extension );
  if ( normalize )
    normalize( img );
  updateMetaDataCache( view, (int)d.dimension( 0 ), (int)d.dimension( 1 ), (int)d.dimension( 2 ), dv.dimension( 0 ), dv.dimension( 1 ), dv.dimension( 2 ) );
  return img;
}

@Override
public RandomAccessibleInterval< UnsignedShortType > getImage( final ViewId view )
{
  final BasicViewDescription< ? > vd = sd.getViewDescriptions().get( view );
  final Dimensions d = vd.getViewSetup().getSize();
  final VoxelDimensions dv = vd.getViewSetup().getVoxelSize();
  final ArrayImg< UnsignedShortType, ? > img = ArrayImgs.unsignedShorts( d.dimension( 0 ), d.dimension( 1 ), d.dimension( 2 ) );
  final String ampOrPhaseDir;
  if ( vd.getViewSetup().getAttribute( Channel.class ).getId() == ampChannelId )
    ampOrPhaseDir = amplitudeDir;
  else if ( vd.getViewSetup().getAttribute( Channel.class ).getId() ==  phaseChannelId )
    ampOrPhaseDir = phaseDir;
  else
    throw new RuntimeException( "viewSetupId=" + view.getViewSetupId() + " is not Amplitude nor phase." );
  populateImage( img, directory, stackDir, ampOrPhaseDir, zPlanes, timepoints.get( view.getTimePointId() ), extension );
  updateMetaDataCache( view, (int)d.dimension( 0 ), (int)d.dimension( 1 ), (int)d.dimension( 2 ), dv.dimension( 0 ), dv.dimension( 1 ), dv.dimension( 2 ) );
  return img;
}

@Override
public ImgPlus< UnsignedShortType > getImage( final int timepointId, final ImgLoaderHint... hints )
{
  ensureExpIsOpen();
  final int channel = setup.getChannel().getId();
  final int illumination = setup.getIllumination().getId();
  final int angle = setup.getAngle().getId();
  final ImagePlus imp = getImagePlus( timepointId );
  final Img< UnsignedShortType > img = ImageJFunctions.wrapShort( imp );
  final String name = getBasename( timepointId, angle, channel, illumination );
  final AxisType[] axes = new AxisType[] { Axes.X, Axes.Y, Axes.Z };
  final float zStretching = ( float ) ( exp.pd / exp.pw );
  final double[] calibration = new double[] { 1, 1, zStretching };
  return new ImgPlus<>( img, name, axes, calibration );
}

channel.getId() == viewDataBeads.getChannel() )

final int oc = old.getViewSetup().getChannel().getId();
  if ( vs.getChannel().getId() == oc )
    vsNew = vs;
final int oc = old.getViewSetup().getChannel().getId();
final int oi = old.getViewSetup().getIllumination().getId();
  if ( vs.getChannel().getId() == oc && vs.getIllumination().getId() == oi )
    vsNew = vs;

  private ImagePlus getImagePlus( final int timepointId )
  {
    final int channel = setup.getChannel().getId();
    final int illumination = setup.getIllumination().getId();
    final int angle = setup.getAngle().getId();
    final int s = exp.sampleStart;
    final int r = exp.regionStart;
    final int f = exp.frameStart;
    final int zMin = exp.planeStart;
    final int zMax = exp.planeEnd;
    final int xMin = 0;
    final int xMax = exp.w - 1;
    final int yMin = 0;
    final int yMax = exp.h - 1;
    ImagePlus imp;
    if ( hasAlternatingIllumination )
    {
      final int zStep = 2;
      if ( illumination == 0 )
        imp = exp.openNotProjected( s, timepointId, timepointId, r, angle, channel, zMin, zMax - 1, zStep, f, f, yMin, yMax, xMin, xMax, SPIMExperiment.X, SPIMExperiment.Y, SPIMExperiment.Z, false );
      else
        imp = exp.openNotProjected( s, timepointId, timepointId, r, angle, channel, zMin + 1, zMax, zStep, f, f, yMin, yMax, xMin, xMax, SPIMExperiment.X, SPIMExperiment.Y, SPIMExperiment.Z, false );
    }
    else
    {
      imp = exp.openNotProjected( s, timepointId, timepointId, r, angle, channel, zMin, zMax, f, f, yMin, yMax, xMin, xMax, SPIMExperiment.X, SPIMExperiment.Y, SPIMExperiment.Z, false );
    }
    return imp;
  }
}

final int c = vd.getViewSetup().getAttribute( Channel.class ).getId();
final int i = vd.getViewSetup().getAttribute( Illumination.class ).getId();