Make InCarta HCS format work, #1137

src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java

@@ -44,7 +44,7 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
-@Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Transform>Registration - Manual")
+@Plugin(type = BdvPlaygroundActionCommand.class, attrs = {}, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Transform>Registration - Manual")
 public class ManualTransformationCommand extends AbstractTransformationCommand
 {
 

src/main/java/org/embl/mobie/command/open/OpenBlobsCommand.java

@@ -0,0 +1,47 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2024 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.command.open;
+
+import ij.IJ;
+import org.embl.mobie.command.CommandConstants;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
+@Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN + "Open Blobs..." )
+public class OpenBlobsCommand implements Command {
+
+	static { net.imagej.patcher.LegacyInjector.preinit(); }
+
+	@Override
+	public void run()
+	{
+		IJ.run("Blobs (25K)");
+	}
+
+}

src/main/java/org/embl/mobie/command/open/OpenImageAndLabelsCommand.java

@@ -60,7 +60,6 @@ public class OpenImageAndLabelsCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
-	// FIXME: What would happen here if the user chooses GridType.None ?
 	@Parameter( label = "Grid", description = MoBIEHelper.GRID_TYPE_HELP )
 	public GridType gridType = GridType.Transformed;
 

src/main/java/org/embl/mobie/lib/hcs/HCSPattern.java

@@ -42,7 +42,8 @@ public enum HCSPattern
 	IncuCyteRaw,
 	InCell, // https://github.com/embl-cba/plateviewer/issues/45
 	MolecularDevices,
-	YokogawaCQ1;
+	YokogawaCQ1,
+	InCarta;
 
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 
@@ -101,6 +102,13 @@ public enum HCSPattern
 	public static final String INCELL = ".*(?<"+WELL+">[A-Z]{1} - [0-9]{2})\\(fld (?<"+SITE+">[0-9]{1}) (?<"+CHANNEL+">.*)\\).tif";
 
 
+	/*
+	example:
+	t1_D04_s1_w1_z3.tif
+	well = D04, site = 1, channel = 1, slice = 3
+	 */
+	public static final String INCARTA = ".*_(?<"+WELL+">[A-Z][0-9]{2})_s(?<"+SITE+">[0-9])_w(?<"+CHANNEL+">[0-9])_z(?<"+SLICE+">[0-9]).tif";
+
 	/*
 	example:
 	W0018F0001T0001Z001C1.tif
@@ -147,6 +155,8 @@ private Matcher getMatcher( String path )
 				return Pattern.compile( INCUCYTE_RAW ).matcher( path );
 			case YokogawaCQ1:
 				return Pattern.compile( YOKOGAWACQ1 ).matcher( path );
+			case InCarta:
+				return Pattern.compile( INCARTA ).matcher( path );
 			default:
 			case IncuCyte:
 				return Pattern.compile( INCUCYTE ).matcher( path );
@@ -233,6 +243,7 @@ private boolean hasChannels()
 			case Operetta:
 			case MolecularDevices:
 			case IncuCyteRaw:
+			case InCarta:
 				return true;
 			default:
 				return false;
@@ -247,6 +258,7 @@ public boolean hasT()
 			case Operetta:
 			case MolecularDevices:
 			case InCell:
+			case InCarta: // TODO could be made true
 				return false;
 			default:
 				return true;
@@ -262,6 +274,7 @@ public boolean hasZ()
 		switch ( this )
 		{
 			case YokogawaCQ1:
+			case InCarta:
 				return true;
 			default:
 				return false;

src/main/java/org/embl/mobie/lib/hcs/Plate.java

@@ -158,16 +158,11 @@ else if ( hcsPattern.equals( HCSPattern.YokogawaCQ1 ) )
 			}
 			else if ( hcsPattern.equals( HCSPattern.MolecularDevices ) )
 			{
-				try
-				{
-					imageDataFormat = ImageDataFormat.Tiff;
-					ImagePlus imagePlus = IOHelper.openTiffFromFile( imagePaths.get( 0 ) );
-				}
-				catch ( Exception e )
-				{
-					imageDataFormat = ImageDataFormat.BioFormats;
-					ImagePlus imagePlus = IOHelper.openWithBioFormatsFromFile( imagePaths.get( 0 ), 0 );
-				}
+				imageDataFormat = ImageDataFormat.Tiff;
+			}
+			else if ( hcsPattern.equals( HCSPattern.InCarta ) )
+			{
+				imageDataFormat = ImageDataFormat.Tiff;
 			}
 		}
 		IJ.log( "Found " + imagePaths.size() + " image file(s) in " + ( System.currentTimeMillis() - start ) + " ms." );

src/test/java/develop/hcs/HCSInCarta.java

@@ -0,0 +1,45 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2024 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 develop.hcs;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.command.open.OpenHCSDatasetCommand;
+
+public class HCSInCarta
+{
+    public static void main( String[] args )
+    {
+        final ImageJ imageJ = new ImageJ();
+        imageJ.ui().showUI();
+
+        OpenHCSDatasetCommand command = new OpenHCSDatasetCommand();
+        command.hcsDirectory = "/Users/tischer/Downloads/timepoint0";
+        command.run();
+    }
+}

src/test/java/org/embl/mobie/lib/hcs/HCSPatternTest.java

@@ -42,11 +42,16 @@ class HCSPatternTest
 	private static final String incucyteRaw = "/Users/tischer/Downloads/incu-test-data/2207/19/1110/262/B3-1-C2.tif";
 	private static final String incell = "A - 01(fld 1 wv Green - dsRed z 3).tif";
 
+	private static final String incarta = "t1_D04_s1_w1_z3.tif";
+
 	private static final String yokogawaCQ1 = "W0018F0001T0001Z001C1.tif";
 
 	@Test
 	void fromPath()
 	{
+		final HCSPattern incarta = HCSPattern.fromPath( HCSPatternTest.incarta );
+		assertEquals( incarta, HCSPattern.InCarta );
+
 		final HCSPattern operetta = HCSPattern.fromPath( HCSPatternTest.operetta );
         assertEquals( operetta, HCSPattern.Operetta );
 

src/test/java/projects/microbial_predation/MicrobialPredation.java

@@ -27,5 +27,8 @@ public static void main( String[] args )
         command.spatialCalibration = SpatialCalibration.FromTable;
 
         command.run();
+
+        // https://forum.image.sc/t/make-fiji-not-quit-when-launching-a-macro-headless/97814
+        // run("Open Image and Labels...", "image=/Volumes/Microbial_Predation_Analysis_Dev/Interval_output/Source/.*.tif labels=/Volumes/Microbial_Predation_Analysis_Dev/Interval_output/.*_profile_labels.tif table=/Volumes/Microbial_Predation_Analysis_Dev/Interval_output/.*_measurements.csv spatialcalibration=FromTable gridtype=Transformed");
     }
 }

src/test/java/projects/microbial_predation/view-in-mobie.ijm

@@ -0,0 +1 @@
+run("Open Image and Labels...", "image=/Volumes/Microbial_Predation_Analysis_Dev/Interval_output/Source/.*.tif labels=/Volumes/Microbial_Predation_Analysis_Dev/Interval_output/.*_profile_labels.tif table=/Volumes/Microbial_Predation_Analysis_Dev/Interval_output/.*_measurements.csv spatialcalibration=FromTable gridtype=Transformed");