From 438a2e2a2f1bd0c4a9df52a13e6c8b0dada8e2de Mon Sep 17 00:00:00 2001
From: Tiago Ferreira <tiago.tferr@gmail.com>
Date: Sat, 14 Sep 2024 09:09:25 -0400
Subject: [PATCH] Color mapping of paths: disable non-applicable option in GUI
 prompts

---
 .../java/sc/fiji/snt/analysis/SkeletonConverter.java     | 4 ++--
 src/main/java/sc/fiji/snt/gui/cmds/FigCreatorCmd.java    | 9 +++++++++
 src/main/java/sc/fiji/snt/plugin/TreeMapperCmd.java      | 1 +
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/main/java/sc/fiji/snt/analysis/SkeletonConverter.java b/src/main/java/sc/fiji/snt/analysis/SkeletonConverter.java
index 351c840d..f3bd4a49 100644
--- a/src/main/java/sc/fiji/snt/analysis/SkeletonConverter.java
+++ b/src/main/java/sc/fiji/snt/analysis/SkeletonConverter.java
@@ -690,8 +690,8 @@ public void setMaxConnectDist(double maxConnectDist) {
 	private void assignToImage(final Tree tree) {
 		final String fProp = imp.getProp("extracted-frame");
 		final String cProp = imp.getProp("extracted-channel");
-		final int f = (fProp == null) ? 1 : Integer.valueOf(fProp);
-		final int c = (cProp == null) ? 1 : Integer.valueOf(cProp);
+		final int f = (fProp == null) ? 1 : Integer.parseInt(fProp);
+		final int c = (cProp == null) ? 1 : Integer.parseInt(cProp);
 		tree.list().forEach(path -> path.setCTposition(c, f));
 		tree.assignImage(imp);
 	}
diff --git a/src/main/java/sc/fiji/snt/gui/cmds/FigCreatorCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/FigCreatorCmd.java
index 68a8da43..f5420436 100644
--- a/src/main/java/sc/fiji/snt/gui/cmds/FigCreatorCmd.java
+++ b/src/main/java/sc/fiji/snt/gui/cmds/FigCreatorCmd.java
@@ -87,6 +87,9 @@ public class FigCreatorCmd extends CommonDynamicCmd {
 	@Parameter(required = false)
 	boolean noRasterOutput;
 
+	@Parameter(required = false)
+	boolean noGeodesicTransformation;
+
 	@SuppressWarnings("unused")
 	private void init() {
 		super.init(false);
@@ -107,6 +110,12 @@ private void init() {
 			choices.remove(0);
 			mi.setChoices(choices);
 		}
+		if (noGeodesicTransformation) {
+			final MutableModuleItem<String> mi = (MutableModuleItem<String>) getInfo().getInput("uprightRotation", String.class);
+			final ArrayList<String> choices = new ArrayList<>(mi.getChoices());
+			choices.remove(1);
+			mi.setChoices(choices);
+		}
 	}
 
 
diff --git a/src/main/java/sc/fiji/snt/plugin/TreeMapperCmd.java b/src/main/java/sc/fiji/snt/plugin/TreeMapperCmd.java
index 85352b35..52d68124 100644
--- a/src/main/java/sc/fiji/snt/plugin/TreeMapperCmd.java
+++ b/src/main/java/sc/fiji/snt/plugin/TreeMapperCmd.java
@@ -141,6 +141,7 @@ public void run() {
 			inputs.put("trees", trees);
 			inputs.put("mapper", mapper);
 			inputs.put("noRasterOutput", true);
+			inputs.put("noGeodesicTransformation", onlyConnectivitySafeMetrics);
 			getContext().getService(CommandService.class).run(FigCreatorCmd.class, true, inputs);
 		}
 		SNTUtils.log("Finished...");