From c6b5c64bf5c8e037c46317bcf93ae7fc50adf333 Mon Sep 17 00:00:00 2001
From: Christian Tischer <christian.tischer@embl.de>
Date: Thu, 18 Jul 2024 10:27:53 +0200
Subject: [PATCH] Implement TIFF folder opening

---
 .../org/embl/mobie/io/ImageDataFormat.java    |  4 ++
 .../mobie/io/imagedata/TIFFImageData.java     | 16 ++++++-
 src/test/java/develop/FolderOpenerTest.java   | 43 +++++++++++++++++++
 3 files changed, 62 insertions(+), 1 deletion(-)
 create mode 100644 src/test/java/develop/FolderOpenerTest.java

diff --git a/src/main/java/org/embl/mobie/io/ImageDataFormat.java b/src/main/java/org/embl/mobie/io/ImageDataFormat.java
index 9488a48..087a0fc 100644
--- a/src/main/java/org/embl/mobie/io/ImageDataFormat.java
+++ b/src/main/java/org/embl/mobie/io/ImageDataFormat.java
@@ -30,6 +30,8 @@
 
 import com.google.gson.annotations.SerializedName;
 
+import java.io.File;
+
 import static org.embl.mobie.io.ImageDataFormat.Names.*;
 
 /**
@@ -198,6 +200,8 @@ public static ImageDataFormat fromPath(String path)
         final String lowerCase = path.toLowerCase();
         if(lowerCase.contains( ".zarr" ))
             return ImageDataFormat.OmeZarr;
+        else if (new File(path).isDirectory())
+            return ImageDataFormat.Tiff; // assume TIFF image sequence
         else if (lowerCase.endsWith( ".xml" ))
             return ImageDataFormat.Bdv; // TODO: https://github.com/mobie/mobie-io/issues/131
         else if (lowerCase.endsWith( ".ome.tif" ) || lowerCase.endsWith( ".ome.tiff" ) )
diff --git a/src/main/java/org/embl/mobie/io/imagedata/TIFFImageData.java b/src/main/java/org/embl/mobie/io/imagedata/TIFFImageData.java
index ad67252..a726af9 100644
--- a/src/main/java/org/embl/mobie/io/imagedata/TIFFImageData.java
+++ b/src/main/java/org/embl/mobie/io/imagedata/TIFFImageData.java
@@ -4,12 +4,15 @@
 import ch.epfl.biop.bdv.img.imageplus.ImagePlusToSpimData;
 import ij.IJ;
 import ij.ImagePlus;
+import ij.plugin.FolderOpener;
 import mpicbg.spim.data.SpimData;
 import mpicbg.spim.data.generic.AbstractSpimData;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.NumericType;
 import org.embl.mobie.io.util.IOHelper;
 
+import java.io.File;
+
 public class TIFFImageData< T extends NumericType< T > & NativeType< T > > extends SpimDataImageData< T >
 {
     public TIFFImageData( String uri, SharedQueue sharedQueue )
@@ -19,7 +22,18 @@ public TIFFImageData( String uri, SharedQueue sharedQueue )
             @Override
             public AbstractSpimData< ? > open( String uri )
             {
-                ImagePlus imagePlus = IJ.openVirtual( uri );
+                ImagePlus imagePlus;
+                if ( new File( uri ).isDirectory() )
+                {
+                    imagePlus = FolderOpener.open(
+                            uri,
+                            "virtual filter=(.*.tif.*)");
+                }
+                else
+                {
+                    imagePlus = IJ.openVirtual( uri );
+                }
+
                 //ImagePlus imagePlus = IOHelper.openTiffFromFile( uri );
                 return ImagePlusToSpimData.getSpimData( imagePlus );
             }
diff --git a/src/test/java/develop/FolderOpenerTest.java b/src/test/java/develop/FolderOpenerTest.java
new file mode 100644
index 0000000..f188849
--- /dev/null
+++ b/src/test/java/develop/FolderOpenerTest.java
@@ -0,0 +1,43 @@
+package develop;
+
+import bdv.cache.SharedQueue;
+import bdv.util.BdvFunctions;
+import bdv.viewer.Source;
+import ij.ImagePlus;
+import ij.plugin.FolderOpener;
+import net.imglib2.Volatile;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.NumericType;
+import net.imglib2.util.Pair;
+import org.embl.mobie.io.ImageDataFormat;
+import org.embl.mobie.io.ImageDataOpener;
+import org.embl.mobie.io.imagedata.ImageData;
+import org.embl.mobie.io.imagedata.TIFFImageData;
+
+import java.io.File;
+import java.util.Arrays;
+
+public class FolderOpenerTest
+{
+    public static < T extends NumericType< T > & NativeType< T > > void main( String[] args )
+    {
+
+        String path = "/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/collections/mri-stack/";
+
+        path = "/Volumes/emcf/ronchi/MRC-MM/aligned/G0";
+//        ImagePlus imp = FolderOpener.open(
+//                path,
+//                "virtual filter=(.*.tif.*)");
+//        imp.show();
+
+        ImageData< T > imageData = ImageDataOpener.open( path );
+        Pair< Source< T >, Source< ? extends Volatile< T > > > sourcePair = imageData.getSourcePair( 0 );
+
+        BdvFunctions.show( sourcePair.getB() );
+
+//        boolean directory = new File( "https://sgsdfgdsf/sfsgd" ).isDirectory();
+//        TIFFImageData< ? > imageData = new TIFFImageData<>( path, new SharedQueue( 1 ) );
+//        Source< ? > source = imageData.getSourcePair( 0 ).getA();
+//        System.out.println( Arrays.toString( source.getSource( 0,0 ).dimensionsAsLongArray() ) );
+    }
+}