protected static String[] buildTimepointList( final List< TimePoint > tpList, final boolean addTitle ) { final String[] timepoints = new String[ tpList.size() ]; for ( int i = 0; i < timepoints.length; ++i ) if ( addTitle ) timepoints[ i ] = "Timepoint " + tpList.get( i ).getName(); else timepoints[ i ] = tpList.get( i ).getName(); return timepoints; }
protected String[] assembleTimepoints( final List< TimePoint > timepoints ) { final String[] tps = new String[ timepoints.size() ]; for ( int t = 0; t < tps.length; ++t ) tps[ t ] = timepoints.get( t ).getName(); return tps; }
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; } /*
protected static String[] assembleTimepoints( final TimePoints timepoints ) { final String[] tps = new String[ timepoints.size() ]; for ( int t = 0; t < tps.length; ++t ) tps[ t ] = timepoints.getTimePointsOrdered().get( t ).getName(); return tps; }
/** * Update data to show in the overlay. */ public synchronized void setViewerState( final ViewerState state ) { synchronized ( state ) { final List< SourceState< ? > > sources = state.getSources(); if ( ! sources.isEmpty() ) sourceName = sources.get( state.getCurrentSource() ).getSpimSource().getName(); else sourceName = ""; final List< SourceGroup > groups = state.getSourceGroups(); final DisplayMode mode = state.getDisplayMode(); if ( ( mode == GROUP || mode == FUSEDGROUP ) && ! groups.isEmpty() ) groupName = groups.get( state.getCurrentGroup() ).getName(); else groupName = ""; final int t = state.getCurrentTimepoint(); if ( timePointsOrdered != null && t >= 0 && t < timePointsOrdered.size() ) timepointString = String.format( "t = %s", timePointsOrdered.get( t ).getName() ); else timepointString = String.format( "t = %d", t ); } } }
return DisplayImage.getImagePlusInstance( img, false, "tp: " + viewDescription.getTimePoint().getName() + " viewSetup: " + viewDescription.getViewSetupId(), Double.NaN, Double.NaN ); else return DisplayImage.getImagePlusInstance( img, false, "tp: " + viewDescription.getTimePoint().getName() + " viewSetup: " + viewDescription.getViewSetupId(), minIntensity, maxIntensity );
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[] timepointNames = new String[ timepoints.size() ]; for ( int i = 0; i < timepointNames.length; ++i ) timepointNames[ i ] = result.getTimePointsToProcess().get( i ).getName();
" 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() + ">]" );
t = Integer.parseInt( viewDescription.getTimePoint().getName() );
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() + " timepoint: " + vd.getTimePoint().getName() + " angle: " + vd.getViewSetup().getAngle().getName() + " channel: " + vd.getViewSetup().getChannel().getName() +