Implement improve image path parsing for tables

src/main/java/org/embl/mobie/lib/color/lut/GlasbeyARGBLut.java

@@ -31,6 +31,7 @@
 import net.imglib2.type.numeric.ARGBType;
 
 import java.util.ArrayList;
+import java.util.concurrent.ExecutionException;
 
 /**
  * Modified version of Glasbey LUT,
@@ -62,8 +63,15 @@ public GlasbeyARGBLut( int alpha )
 	@Override
 	public int getARGB( double x )
 	{
-		final int index = ( int ) Math.ceil( x * ( numColors - 1 ) );
-		return indices.get( index );
+		try
+		{
+			final int index = ( int ) Math.ceil( x * ( numColors - 1 ) );
+			return indices.get( index );
+		}
+		catch ( Exception e )
+		{
+			throw new RuntimeException( e  );
+		}
 	}
 
 	@Override

src/main/java/org/embl/mobie/lib/files/ImageFileSources.java

@@ -31,6 +31,7 @@
 import ij.IJ;
 import net.imglib2.realtransform.AffineTransform3D;
 import org.apache.commons.io.FilenameUtils;
+import org.embl.mobie.io.util.IOHelper;
 import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.io.TableImageSource;
 import org.embl.mobie.lib.source.Metadata;
@@ -111,6 +112,7 @@ public ImageFileSources( String name, Table table, String imageColumn, Integer c
 		nameToPath = new LinkedHashMap<>(); // needed for joining the tables below when creating the region table
 
 		int numRows = table.rowCount();
+
 		if ( imageColumn.contains( "_IMG" )  )
 		{
 			// Automic table
@@ -132,26 +134,20 @@ public ImageFileSources( String name, Table table, String imageColumn, Integer c
 				}
 			}
 		}
-		else if ( imageColumn.startsWith( "FileName_" ) )
+		else if ( isCellProfilerColumn( imageColumn, table ) )
 		{
-			TableImageSource tableImageSource = new TableImageSource( imageColumn );
-
-			// Deal with CellProfiler tables
-			String postfix = tableImageSource.columnName.substring("FileName_".length());
+			String postfix = imageColumn.substring("FileName_".length());
 			String folderColumn = "PathName_" + postfix;
-			if (table.containsColumn( folderColumn ) ) {
-				StringColumn absolutePathColumn =
-						table.stringColumn( folderColumn )
-								.concatenate( File.separator )
-								.concatenate( table.stringColumn( tableImageSource.columnName ) );
-				absolutePathColumn.setName("AbsolutePath_" + postfix);
-				table.addColumns(absolutePathColumn);
-				root = null; // the paths are now absolute
-				tableImageSource = new TableImageSource( tableImageSource.name, "AbsolutePath_" + postfix, tableImageSource.channelIndex, pathMapping );
-			}
-
-			imageFileSources.add( new ImageFileSources( tableImageSource.name, table, tableImageSource.columnName, tableImageSource.channelIndex, root, pathMapping, gridType ) );
 
+			for ( int rowIndex = 0; rowIndex < numRows; rowIndex++ )
+			{
+				String fileName = table.getString( rowIndex, imageColumn );
+				String folder = table.getString( rowIndex, folderColumn );
+				String path = IOHelper.combinePath( folder, fileName );
+				String imageName = createImageName( channelIndex, fileName );
+				nameToFullPath.put( imageName, applyPathMapping( pathMapping, path ) );
+				nameToPath.put( imageName, fileName );
+			}
 		}
 		else
 		{
@@ -171,6 +167,17 @@ else if ( imageColumn.startsWith( "FileName_" ) )
 		dealWithTimepointsInObjectTableIfNeeded( name, table, imageColumn );
 	}
 
+	protected static boolean isCellProfilerColumn( String column, Table table )
+	{
+		if ( ! column.startsWith( "FileName_" ) ) return false;
+
+		String postfix = column.substring("FileName_".length());
+		String folderColumn = "PathName_" + postfix;
+		boolean containsFolderColumn = table.containsColumn( folderColumn );
+
+		return containsFolderColumn;
+	}
+
 	protected static List< String > getFullPaths( String regex, String root )
 	{
 		if ( root != null )

src/main/java/org/embl/mobie/lib/files/LabelFileSources.java

@@ -77,15 +77,15 @@ public LabelFileSources( String name, Table table, String columnName, Integer ch
 		}
 	}
 
-	public LabelFileSources( String name, String labelsPath, Integer channelIndex, String root, String pathMapping, GridType grid )
+	public LabelFileSources( String name, String labelsPath, Integer channelIndex, String root, GridType grid )
 	{
-		super( name, labelsPath, channelIndex, root, pathMapping, grid );
+		super( name, labelsPath, channelIndex, root, grid );
 	}
 
 
-	public LabelFileSources( String name, String path, Integer channelIndex, String labelTablePath, String root, String pathMapping, GridType grid )
+	public LabelFileSources( String name, String path, Integer channelIndex, String labelTablePath, String root, GridType grid )
 	{
-		super( name, path, channelIndex, root, pathMapping, grid );
+		super( name, path, channelIndex, root, grid );
 
 		final List< String > labelTablePaths = getFullPaths( labelTablePath, root );
 		final ArrayList< String > labelMaskNames = new ArrayList<>( nameToFullPath.keySet() );

src/main/java/org/embl/mobie/lib/files/SourcesFromPathsCreator.java

@@ -43,15 +43,13 @@ public class SourcesFromPathsCreator
 
 	public SourcesFromPathsCreator( List < String > imagePaths, List < String > labelPaths, List < String > labelTablePaths, String root, GridType grid )
 	{
-		// FIXME: Remove all the pathMapping from the Constructors here!
-
 		// images
 		//
 		imageSources = new ArrayList<>();
 		for ( String imagePath : imagePaths )
 		{
 			final FileImageSource fileImageSource = new FileImageSource( imagePath );
-			imageSources.add( new ImageFileSources( fileImageSource.name, fileImageSource.path, fileImageSource.channelIndex, root, null, grid ) );
+			imageSources.add( new ImageFileSources( fileImageSource.name, fileImageSource.path, fileImageSource.channelIndex, root, grid ) );
 		}
 
 		// segmentation images
@@ -64,11 +62,11 @@ public SourcesFromPathsCreator( List < String > imagePaths, List < String > labe
 			if ( labelTablePaths.size() > labelSourceIndex )
 			{
 				final String labelTablePath = labelTablePaths.get( labelSourceIndex );
-				labelSources.add( new LabelFileSources( fileImageSource.name, fileImageSource.path, fileImageSource.channelIndex, labelTablePath, root, null, grid ) );
+				labelSources.add( new LabelFileSources( fileImageSource.name, fileImageSource.path, fileImageSource.channelIndex, labelTablePath, root, grid ) );
 			}
 			else
 			{
-				labelSources.add( new LabelFileSources( fileImageSource.name, fileImageSource.path, fileImageSource.channelIndex, root, null, grid ) );
+				labelSources.add( new LabelFileSources( fileImageSource.name, fileImageSource.path, fileImageSource.channelIndex, root, grid ) );
 			}
 		}
 	}