protected String[] assembleChannels( final List< Channel > channels ) { final String[] chs = new String[ channels.size() ]; for ( int t = 0; t < chs.length; ++t ) chs[ t ] = channels.get( t ).getName(); return chs; }
public String dialogName() { String s = ""; s += ( ts.size() > 1 ) ? "all_timepoints" : "timepoint_" + ts.iterator().next().getName(); s += ( cs.size() > 1 ) ? "_all_channels" : "_channel_" + cs.iterator().next().getName(); s += ( is.size() > 1 ) ? "_all_illuminations" : "_illumination_" + is.iterator().next().getName(); s += ( as.size() > 1 ) ? "_all_angles" : "_angle_" + as.iterator().next().getName(); return s; } /*
private static String createSetupName( final BasicViewSetup setup ) { if ( setup.hasName() ) return setup.getName(); String name = ""; final Angle angle = setup.getAttribute( Angle.class ); if ( angle != null ) name += ( name.isEmpty() ? "" : " " ) + "a " + angle.getName(); final Channel channel = setup.getAttribute( Channel.class ); if ( channel != null ) name += ( name.isEmpty() ? "" : " " ) + "c " + channel.getName(); return name; }
public static void main( String args[] ) { new ImageJ(); IOFunctions.printIJLog = true; final LoadParseQueryXML lpq = new LoadParseQueryXML(); final ArrayList< String > queryFor = new ArrayList< String >(); queryFor.add( "Timepoint" ); queryFor.add( "channel" ); queryFor.add( "angle" ); queryFor.add( "Tile" ); queryFor.add( "illumination" ); lpq.queryXML( true, true, true, true, true ); for ( final TimePoint i : lpq.getTimePointsToProcess() ) System.out.println( i.getId() ); for ( final ViewSetup v : lpq.getViewSetupsToProcess() ) { System.out.println( v.getId() + " " + v.getAngle().getName() + " " + v.getChannel().getName() + " " + v.getIllumination().getName() ); } } }
protected String nameForGroup( final Group< ViewDescription > group ) { final ViewDescription vd1 = group.iterator().next(); String name = "TP=" + vd1.getTimePointId() + " Angle=" + vd1.getViewSetup().getAngle().getName() + " Channel=" + vd1.getViewSetup().getChannel().getName(); if ( !groupIllums ) name += " Illum=" + vd1.getViewSetup().getChannel().getName(); if ( !groupTiles ) name += " Tile=" + vd1.getViewSetup().getTile().getName(); return name; }
protected File getFile( final ViewId view ) { final TimePoint tp = sequenceDescription.getTimePoints().getTimePoints().get( view.getTimePointId() ); final BasicViewSetup vs = sequenceDescription.getViewSetups().get( view.getViewSetupId() ); final String timepoint = tp.getName(); final String angle = vs.getAttribute( Angle.class ).getName(); final String channel = vs.getAttribute( Channel.class ).getName(); final String illum = vs.getAttribute( Illumination.class ).getName(); final String tile = vs.getAttribute( Tile.class ).getName(); final String[] fileName = StackList.getFileNamesFor( fileNamePattern, replaceTimepoints, replaceChannels, replaceIlluminations, replaceAngles, replaceTiles, timepoint, channel, illum, angle, tile, numDigitsTimepoints, numDigitsChannels, numDigitsIlluminations, numDigitsAngles, numDigitsTiles ); // check which of them exists and return it for ( final String fn : fileName ) { final File f = new File( path, fn ); if ( f.exists() ) return f; else IOFunctions.println( "File '" + f.getAbsolutePath() + "' does not exist." ); } IOFunctions.println( "Could not find file for tp=" + timepoint + ", angle=" + angle + ", channel=" + channel + ", ill=" + illum + ", tile=" + tile ); return null; }
IOFunctions.println( "Reseting model to identity transform for timepoint " + t.getName() + ", channel " + c.getName() + ", illum " + i.getName() + ", angle " + a.getName() ); setModelToIdentity( spimData, vd ); IOFunctions.println( "Reseting model to calibration for timepoint " + t.getName() + ", channel " + c.getName() + ", illum " + i.getName() + ", angle " + a.getName() ); setModelToCalibration( spimData, vd, minResolution ); IOFunctions.println( "Applying model " + Util.printCoordinates( v ) + " (" + modelDesc + ") to timepoint " + t.getName() + ", channel " + c.getName() + ", illum " + i.getName() + ", angle " + a.getName() );
final String[] channelNames = new String[ channels.size() ]; for ( int i = 0; i < channels.size(); ++i ) channelNames[ i ] = channels.get( i ).getName();
filename += "_Ch" + viewDescription.getViewSetup().getChannel().getName();
gdp.addMessage( "Channel: " + c.getName() + ", Illumination: " + ill.getName() + ":" ); gdp.addFileField( "Bright_Image", bright ); gdp.addFileField( "Dark_Image", dark );
" channel: " + ((ViewSetup)vs).getChannel().getName() + " illum: " + ((ViewSetup)vs).getIllumination().getName() + ", present at timepoint: " + t.getName() +
new ViewSetup( newViewSetupId++, c.getName(), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", new double[] { downsampling, downsampling, downsampling * anisoF } ), new ViewSetup( newViewSetupId++, channels.get( c ).getName() + "_" + illums.get( i ).getName(), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", new double[] { downsampling, downsampling, downsampling * anisoF } ),
" angle=" + a.getName() + " ch=" + c.getName() + " illum=" + i.getName() + " tp=" + t.getName() + " type=" + meta.pixelTypeString() + " img=" + img.getClass().getSimpleName() + "<" + type.getClass().getSimpleName() + ">]" );
" angle=" + a.getName() + " ch=" + c.getName() + " illum=" + i.getName() + " tp=" + t.getName() + " tile=" + tile.getName() + " type=" + FormatTools.getPixelTypeString( reader.getPixelType()) + " img=" + img.getClass().getSimpleName() + "<" + type.getClass().getSimpleName() + ">]" );
new ViewSetup( newViewSetupId++, c.getName(), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", Util.getArrayFromValue( downsampling, 3 ) ), new ViewSetup( newViewSetupId++, channels.get( c ).getName() + "_" + illums.get( i ).getName(), fusion.getDownsampledBoundingBox(), new FinalVoxelDimensions( "px", Util.getArrayFromValue( downsampling, 3 ) ),
final ViewSetup targetVS = targetVD.getViewSetup(); IOFunctions.println( "Source viewId t=" + sourceVD.getTimePoint().getName() + ", ch=" + sourceVS.getChannel().getName() + ", ill=" + sourceVS.getIllumination().getName() + ", angle=" + sourceVS.getAngle().getName() ); IOFunctions.println( "Target viewId t=" + targetVD.getTimePoint().getName() + ", ch=" + targetVS.getChannel().getName() + ", ill=" + targetVS.getIllumination().getName() + ", angle=" + targetVS.getAngle().getName() );
" timepoint: " + vd.getTimePoint().getName() + " angle: " + vd.getViewSetup().getAngle().getName() + " channel: " + vd.getViewSetup().getChannel().getName() + " illum: " + vd.getViewSetup().getIllumination().getName() ); " timepoint: " + vd.getTimePoint().getName() + " angle: " + vd.getViewSetup().getAngle().getName() + " channel: " + vd.getViewSetup().getChannel().getName() + " illum: " + vd.getViewSetup().getIllumination().getName() );