Enable opening of the Microglia data

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>4.1.4-SNAPSHOT</version>
+    <version>4.1.4</version>
 
 
     <!-- force javadoc generation to fetch errors:    -->

src/main/java/org/embl/mobie/lib/SourcesFromTableCreator.java

@@ -104,11 +104,7 @@ public SourcesFromTableCreator( String tablePath, List< String > imageColumns, L
 		//
 		int numSources = imageFileSources.get( 0 ).getSources().size();
 
-		if ( numSources == 1 )
-		{
-			// no region table and no grid view needed
-		}
-		else if ( table.rowCount() == numSources )
+		if ( table.rowCount() == numSources )
 		{
 			// the input table is an image table and
 			// can thus be used as the region table

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

@@ -111,7 +111,11 @@ public void addDataAndDisplaysAndViews( Dataset dataset )
 			}
 		}
 
+		addGridView( dataset, allSources );
+	}
 
+	private void addGridView( Dataset dataset, ArrayList< ImageFileSources > allSources )
+	{
 		RegionDisplay< AnnotatedRegion > regionDisplay = null;
 		final List< Display< ? > > displays = new ArrayList<>();
 		final List< Transformation > transformations = new ArrayList<>();

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

@@ -36,22 +36,18 @@
 import org.embl.mobie.lib.table.ColumnNames;
 import org.embl.mobie.lib.table.TableDataFormat;
 import org.embl.mobie.lib.table.columns.SegmentColumnNames;
-import org.embl.mobie.lib.table.saw.Aggregators;
 import org.embl.mobie.lib.transform.GridType;
 import tech.tablesaw.api.NumberColumn;
 import tech.tablesaw.api.StringColumn;
 import tech.tablesaw.api.Table;
-import tech.tablesaw.columns.Column;
 
 import java.io.File;
-import java.lang.reflect.Executable;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
 import static org.embl.mobie.io.util.IOHelper.getPaths;
-import static tech.tablesaw.aggregate.AggregateFunctions.mean;
 
 public class ImageFileSources
 {

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

@@ -28,6 +28,7 @@
  */
 package org.embl.mobie.lib.files;
 
+import ij.IJ;
 import org.embl.mobie.lib.io.StorageLocation;
 import org.embl.mobie.lib.table.TableDataFormat;
 import org.embl.mobie.lib.table.TableSource;
@@ -44,6 +45,7 @@
 public class LabelFileSources extends ImageFileSources
 {
 	protected Map< String, TableSource > nameToLabelTable = new LinkedHashMap<>();
+	private static boolean logLabelParsingError = true;
 
 	public LabelFileSources( String name, Table table, String columnName, Integer channelIndex, String root, GridType gridType, boolean useTableForSegments )
 	{
@@ -66,9 +68,11 @@ public LabelFileSources( String name, Table table, String columnName, Integer ch
 			}
 			else
 			{
-				/*
-				The table does not contain any segment information that can be parsed.
-				 */
+				if ( logLabelParsingError )
+				{
+					IJ.log( "[WARNING] The table does not contain parseable segments (labels) information."  );
+					logLabelParsingError = false;
+				}
 			}
 		}
 	}

src/main/java/org/embl/mobie/lib/source/Metadata.java

@@ -28,8 +28,13 @@
  */
 package org.embl.mobie.lib.source;
 
+import IceInternal.Ex;
 import ij.IJ;
 import ij.ImagePlus;
+import ij.plugin.ContrastEnhancer;
+import ij.process.ImageStatistics;
+
+import static ij.measure.Measurements.MIN_MAX;
 
 public class Metadata
 {
@@ -39,18 +44,31 @@ public class Metadata
 	public Integer numTimePoints = null;
 	public Integer numZSlices = 1;
 	public Integer numChannelsContainer = 1; // in MoBIE each image has jsut one channel, but the container could have multiple
+	private static boolean logBFError = true;
 
 	public Metadata()
 	{
 	}
 
 	public Metadata( ImagePlus imagePlus )
 	{
-		color = "White"; // TODO: why not extract the color?
-		// we could use more direct methods:
-		// https://imagej.nih.gov/ij/developer/source/ij/plugin/ContrastEnhancer.java.html
-		IJ.run( imagePlus, "Enhance Contrast", "saturated=0.35" );
-		contrastLimits = new double[]{ imagePlus.getDisplayRangeMin(), imagePlus.getDisplayRangeMax() };
+		color = "White"; // TODO: why not also extract the color?
+
+		try
+		{
+			ImageStatistics statistics = ImageStatistics.getStatistics( imagePlus.getProcessor(), MIN_MAX, null );
+			new ContrastEnhancer().stretchHistogram( imagePlus.getProcessor(), 0.35, statistics );
+		}
+		catch ( Exception e )
+		{
+			if ( logBFError )
+			{
+				// https://forum.image.sc/t/b-c-for-a-whole-virtual-stack-cont/57811/12
+				IJ.log( "[WARNING] Could not determine auto-contrast for some images due to Bio-Formats issue: https://forum.image.sc/t/b-c-for-a-whole-virtual-stack-cont/57811/12" );
+				logBFError = false;
+			}
+		}
+		contrastLimits = new double[]{ imagePlus.getProcessor().getMin(), imagePlus.getProcessor().getMax() };
 		numTimePoints = imagePlus.getNFrames();
 		numZSlices = imagePlus.getNSlices();
 		numChannelsContainer = imagePlus.getNChannels();

src/main/java/org/embl/mobie/lib/table/TableDataFormat.java

@@ -31,6 +31,7 @@
 import com.google.gson.annotations.SerializedName;
 import ij.IJ;
 import org.embl.mobie.lib.table.columns.*;
+import org.embl.mobie.lib.table.saw.TableOpener;
 
 import java.util.Collection;
 
@@ -76,8 +77,9 @@ public String toString()
 
 	public static TableDataFormat fromPath( String path )
 	{
-		if ( path.endsWith( ".csv" ) ) return CSV;
-		if ( path.endsWith( ".tsv" ) ) return TSV;
+		Character delimiter = TableOpener.determineDelimiter( path );
+		if ( delimiter.equals( ',' ) ) return CSV;
+		if ( delimiter.equals( '\t' ) ) return TSV;
 		throw new RuntimeException("Could not determine table format of " + path );
 	}
 
@@ -129,10 +131,14 @@ public static SegmentColumnNames getSegmentColumnNames( Collection< String > col
 
 		if ( CellProfilerSegmentColumnNames.matches( columnNames ) )
 		{
-			IJ.log( "Identified CellProfiler object table." );
 			return new CellProfilerSegmentColumnNames( columnNames );
 		}
 
+		if ( MicrogliaSegmentColumnNames.matches( columnNames ) )
+		{
+			return new MicrogliaSegmentColumnNames();
+		}
+
 		return null;
 	}
 }

src/main/java/org/embl/mobie/lib/table/columns/MicrogliaSegmentColumnNames.java

@@ -0,0 +1,91 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2023 EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.embl.mobie.lib.table.columns;
+
+import java.util.Collection;
+
+/**
+ * https://github.com/embl-cba/microglia-morphometry/tree/main#features
+ *
+ */
+public class MicrogliaSegmentColumnNames implements SegmentColumnNames
+{
+	private static final String NONE = "None";
+	private static final String LABEL_ID = "Object_Label";
+	private static final String[] ANCHOR = { "Centroid_X_Pixel", "Centroid_Y_Pixel", "Centroid_Z_Pixel" };
+	private static final String[] BB_MIN = { NONE, NONE, NONE };
+	private static final String[] BB_MAX = { NONE, NONE, NONE };
+	private static final String TIMEPOINT = "Centroid_Time_Frames";
+
+	@Override
+	public String labelImageColumn()
+	{
+		return NONE;
+	}
+
+	@Override
+	public String labelIdColumn()
+	{
+		return LABEL_ID;
+	}
+
+	@Override
+	public String timePointColumn()
+	{
+		return TIMEPOINT;
+	}
+
+	@Override
+	public String[] anchorColumns()
+	{
+		return ANCHOR;
+	}
+
+	@Override
+	public String[] bbMinColumns()
+	{
+		return BB_MIN;
+	}
+
+	@Override
+	public String[] bbMaxColumns()
+	{
+		return BB_MAX;
+	}
+
+	public static boolean matches( Collection< String > columns )
+	{
+		return columns.contains( LABEL_ID );
+	}
+
+	@Override
+	public boolean timePointsAreOneBased() {
+		return true;
+	}
+}

src/main/java/org/embl/mobie/lib/table/columns/SegmentColumnNames.java

@@ -43,4 +43,8 @@ public interface SegmentColumnNames
 
 	String[] bbMaxColumns();
 
+	default boolean timePointsAreOneBased() {
+		return false;
+	}
+
 }

src/main/java/org/embl/mobie/lib/table/saw/TableOpener.java

@@ -41,6 +41,9 @@
 import tech.tablesaw.api.IntColumn;
 import tech.tablesaw.api.Table;
 import tech.tablesaw.io.csv.CsvReadOptions;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URI;
@@ -176,15 +179,30 @@ public static Table openResultTable( ResultsTable resultsTable )
 		return table;
 	}
 
-	public static Character guessDelimiter( String path )
+	public static Character determineDelimiter( String path )
 	{
 		if ( path.endsWith( ".txt" ) )
 			return '\t';
 
 		if ( path.endsWith( ".tsv" ) )
 			return '\t';
 
-		return ',';
+		try (BufferedReader reader = new BufferedReader(new FileReader(path))) {
+			String firstLine = reader.readLine();
+			if (firstLine != null) {
+				if (firstLine.contains("\t")) {
+					return '\t';
+				} else if (firstLine.contains(",")) {
+					return ',';
+				} else {
+					return ','; // We could also throw and error, but maybe there is only one column ?
+				}
+			}
+		} catch (IOException e) {
+			throw new RuntimeException( e );
+		}
+
+		throw new RuntimeException( "Could not determine table delimiter" );
 	}
 
 	public static Table openDelimitedTextFile( String path, char separator )
@@ -253,6 +271,6 @@ private static String dealWithTwoHeaderRowsIfNeeded( char separator, String cont
 
 	public static Table openDelimitedTextFile( String path )
 	{
-		return openDelimitedTextFile( path, guessDelimiter( path ) );
+		return openDelimitedTextFile( path, determineDelimiter( path ) );
 	}
 }

src/main/java/org/embl/mobie/lib/table/saw/TableSawAnnotatedSegmentCreator.java

@@ -30,6 +30,7 @@
 
 import net.imglib2.FinalRealInterval;
 import org.embl.mobie.lib.table.TableDataFormat;
+import org.embl.mobie.lib.table.columns.MicrogliaSegmentColumnNames;
 import org.embl.mobie.lib.table.columns.SegmentColumnNames;
 import tech.tablesaw.api.Table;
 
@@ -97,8 +98,6 @@ private synchronized void initColumns( Table table )
 		is3D = anchorColumnIndices.length == 3 && anchorColumnIndices[ 2 ] > -1;
 
 		hasBoundingBox = bbMinColumnIndices[ 0 ] > -1;
-
-
 	}
 
 	@Override
@@ -115,6 +114,9 @@ public TableSawAnnotatedSegment create( TableSawAnnotationTableModel< TableSawAn
 
 		int timePoint = timePointColumnIndex > -1 ? table.intColumn( timePointColumnIndex ).get( rowIndex ) : 0;
 
+		if ( timePointColumnIndex > -1 && segmentColumnNames.timePointsAreOneBased()  )
+			timePoint -= 1;
+
 		final FinalRealInterval boundingBox = boundingBox( table, rowIndex );
 
 		// TODO do we want to support missing anchor columns?

src/test/java/projects/OpenVeronicaMicroglia.java

@@ -0,0 +1,22 @@
+package projects;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.MoBIE;
+import org.embl.mobie.command.open.OpenTableCommand;
+
+import java.io.File;
+
+public class OpenVeronicaMicroglia
+{
+    public static void main( String[] args )
+    {
+        new ImageJ().ui().showUI();
+        final OpenTableCommand command = new OpenTableCommand();
+        command.root = new File( "/Users/tischer/Desktop/veronica" );
+        command.table = new File( "/Users/tischer/Desktop/veronica/Intensities c3 pup4 lps.csv" );
+        command.images = "Path_Intensities=Signal";
+        command.labels = "Path_LabelMasks=Segmentations,Path_Skeletons=Skeletons,Path_Annotations=Annotations";
+        command.removeSpatialCalibration = false;
+        command.run();
+    }
+}