Merge branch 'master' of https://github.com/BIOP/ijp-imagetoatlas

BIOP · Sep 12, 2024 · fa2e953 · fa2e953
2 parents e5e2684 + 61348df
commit fa2e953
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Showing 6 changed files with 91 additions and 4 deletions.
diff --git a/message/howtocite.html b/message/howtocite.html
@@ -1,6 +1,7 @@
 <html>
   <body style='font-family:sans-serif; font-size:12px; color:#333333;'>
-  <p style='margin-top:0;'>If you use ABBA for your research, a preprint will soon become available...</p>
-  <p>Don't forget to cite these resources if you use them: atlas dataset, DeepSlice, QuPath.<p/>
+  <p style='margin-top:0;'>If you use ABBA for your research, please cite this preprint:</p>
+  <p><a href="https://doi.org/10.1101/2024.09.06.611625">https://doi.org/10.1101/2024.09.06.611625</a></p>  
+  <p>Also, don't forget to cite the other resources you may be using: atlas dataset, DeepSlice, QuPath.<p/>
   </body>
 </html>
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/ABBACiteInfoCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/ABBACiteInfoCommand.java
@@ -30,7 +30,6 @@ public class ABBACiteInfoCommand implements Command {
     public void run() {
 
         JFrame frame = new JFrame("How to cite");
-        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
         frame.setSize(450, 350);
         frame.setLocationRelativeTo(null); // Center the window
         frame.setIconImage((new ImageIcon(MultiSlicePositioner.class.getResource("/graphics/ABBAFrame.jpg"))).getImage());

diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/SetSlicesDeselectedCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/SetSlicesDeselectedCommand.java
@@ -0,0 +1,39 @@
+package ch.epfl.biop.atlas.aligner.command;
+
+import ch.epfl.biop.atlas.aligner.MultiSlicePositioner;
+import ch.epfl.biop.sourceandconverter.exporter.IntRangeParser;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+import java.util.List;
+
+@SuppressWarnings("CanBeFinal")
+@Plugin(type = Command.class,
+        menuPath = "Plugins>BIOP>Atlas>Multi Image To Atlas>Edit>ABBA - Deselect Slices",
+        description = "Set the slices to deselect.")
+public class SetSlicesDeselectedCommand implements Command {
+
+    @Parameter
+    MultiSlicePositioner mp;
+
+    @Parameter(label = "Slices to deselect, '*' for all slices, comma separated, 0-based")
+    String slices_csv = "*";
+
+    @Override
+    public void run() {
+        if (slices_csv.trim().equals("*")) {
+            slices_csv ="0:-1";
+        }
+        try {
+            List<Integer> indices = new IntRangeParser(slices_csv).get(mp.getSlices().size());
+            for (int index: indices) {
+                mp.getSlices().get(index).deSelect();
+            }
+        } catch (Exception e) {
+            mp.errorMessageForUser.accept("Error during parsing of slice indices", e.getMessage());
+            throw new RuntimeException(e);
+        }
+    }
+
+}
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/SetSlicesSelectedCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/SetSlicesSelectedCommand.java
@@ -0,0 +1,42 @@
+package ch.epfl.biop.atlas.aligner.command;
+
+import ch.epfl.biop.atlas.aligner.MultiSlicePositioner;
+import ch.epfl.biop.atlas.aligner.SliceSources;
+import ch.epfl.biop.sourceandconverter.exporter.IntRangeParser;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+@SuppressWarnings("CanBeFinal")
+@Plugin(type = Command.class,
+        menuPath = "Plugins>BIOP>Atlas>Multi Image To Atlas>Edit>ABBA - Select Slices",
+        description = "Set the slices to select.")
+public class SetSlicesSelectedCommand implements Command {
+
+    @Parameter
+    MultiSlicePositioner mp;
+
+    @Parameter(label = "Slices to select, '*' for all slices, comma separated, 0-based")
+    String slices_csv = "*";
+
+    @Override
+    public void run() {
+        if (slices_csv.trim().equals("*")) {
+            slices_csv ="0:-1";
+        }
+        try {
+            List<Integer> indices = new IntRangeParser(slices_csv).get(mp.getSlices().size());
+            for (int index: indices) {
+                mp.getSlices().get(index).select();
+            }
+        } catch (Exception e) {
+            mp.errorMessageForUser.accept("Error during parsing of slice indices", e.getMessage());
+            throw new RuntimeException(e);
+        }
+    }
+
+}
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/BdvMultislicePositionerView.java b/src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/BdvMultislicePositionerView.java
@@ -58,7 +58,9 @@
 import ch.epfl.biop.atlas.aligner.command.RegisterSlicesElastixSplineCommand;
 import ch.epfl.biop.atlas.aligner.command.RegisterSlicesRemoveLastCommand;
 import ch.epfl.biop.atlas.aligner.command.RotateSlicesCommand;
+import ch.epfl.biop.atlas.aligner.command.SetSlicesDeselectedCommand;
 import ch.epfl.biop.atlas.aligner.command.SetSlicesDisplayRangeCommand;
+import ch.epfl.biop.atlas.aligner.command.SetSlicesSelectedCommand;
 import ch.epfl.biop.atlas.aligner.command.SetSlicesThicknessCommand;
 import ch.epfl.biop.atlas.aligner.command.SetSlicesThicknessMatchNeighborsCommand;
 import ch.epfl.biop.atlas.aligner.command.SliceAffineTransformCommand;
@@ -375,6 +377,8 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
 
         BdvScijavaHelper.addActionToBdvHandleMenu(bdvh,"Slices>Select All Slices [Ctrl+A]",0,() -> msp.getSlices().forEach(SliceSources::select));
         BdvScijavaHelper.addActionToBdvHandleMenu(bdvh,"Slices>Deselect All Slices [Ctrl+Shift+A]",0,() -> msp.getSlices().forEach(SliceSources::deSelect));
+        BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(),"Slices>Select Slices", SetSlicesSelectedCommand.class, "mp", msp);
+        BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(),"Slices>Deselect Slices", SetSlicesDeselectedCommand.class, "mp", msp);
         BdvScijavaHelper.addSeparator(bdvh,"Slices");
         BdvScijavaHelper.addActionToBdvHandleMenu(bdvh,"Slices>Remove Slices",0,() ->
                 msp.getSlices()
@@ -471,7 +475,7 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
         BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>Give your feedback (web)", ABBAUserFeedbackCommand.class);
         BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>About DeepSlice (web)", DeepSliceDocumentationCommand.class);
         BdvScijavaHelper.addSeparator(bdvh,"Help");
-        BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>How to cite ABBA (web)", ABBACiteInfoCommand.class);
+        BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>How to cite ABBA", ABBACiteInfoCommand.class);
 
     }
 

diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/processor/ABBAPostProcessor.java b/src/main/java/ch/epfl/biop/atlas/aligner/processor/ABBAPostProcessor.java
@@ -8,6 +8,7 @@
 import ch.epfl.biop.atlas.aligner.gui.bdv.ABBABdvStartCommand;
 import ch.epfl.biop.atlas.mouse.allen.ccfv3p1.command.AllenBrainAdultMouseAtlasCCF2017v3p1Command;
 import ch.epfl.biop.atlas.scijava.AtlasChooserCommand;
+import ch.epfl.biop.bdv.img.omero.command.OmeroConnectCommand;
 import ch.epfl.biop.scijava.command.bdv.userdefinedregion.GetUserRectangleCommand;
 import org.scijava.Priority;
 import org.scijava.command.CommandInfo;
@@ -56,6 +57,7 @@ static void initializeCommands() {
                 checkedCommands.add(ABBAStateSaveCommand.class.getName());
                 checkedCommands.add(GetUserRectangleCommand.class.getName());
                 checkedCommands.add(DisplaySettingsCommand.class.getName());
+                checkedCommands.add(OmeroConnectCommand.class.getName());
                 initialized = true;
             }
         }