From a26a85e492cae1ad878d20d8600f203e106c05fc Mon Sep 17 00:00:00 2001
From: steffen-klein <steffen.klein@bioquant.uni-heidelberg.de>
Date: Wed, 30 Jun 2021 16:40:25 +0200
Subject: [PATCH] added overlap computation to stitching

---
 .idea/encodings.xml                           | 1 -
 .idea/misc.xml                                | 2 +-
 fiji_plugin/src/main/java/StitchTileScan.java | 2 +-
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.idea/encodings.xml b/.idea/encodings.xml
index 90faf37..c38ffb1 100644
--- a/.idea/encodings.xml
+++ b/.idea/encodings.xml
@@ -2,6 +2,5 @@
 <project version="4">
   <component name="Encoding">
     <file url="file://$PROJECT_DIR$/fiji_plugin/src/main/java" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/fiji_plugin/src/main/resources" charset="UTF-8" />
   </component>
 </project>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
index 41abb8c..cb912a3 100644
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -7,7 +7,7 @@
       </list>
     </option>
   </component>
-  <component name="ProjectRootManager" version="2" languageLevel="JDK_14" project-jdk-name="14" project-jdk-type="JavaSDK">
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_14" project-jdk-name="15" project-jdk-type="JavaSDK">
     <output url="file://$PROJECT_DIR$/out" />
   </component>
 </project>
\ No newline at end of file
diff --git a/fiji_plugin/src/main/java/StitchTileScan.java b/fiji_plugin/src/main/java/StitchTileScan.java
index 47e691c..bd6e837 100644
--- a/fiji_plugin/src/main/java/StitchTileScan.java
+++ b/fiji_plugin/src/main/java/StitchTileScan.java
@@ -149,7 +149,7 @@ public MaxProjection call() throws Exception {
                     String.format("type=[Positions from file] " + "order=[Defined by TileConfiguration] " + "directory=[%s] "
                             + "layout_file=[%s] " + "fusion_method=[Linear Blending] "
                             + "regression_threshold=0.30 " + "max/avg_displacement_threshold=2.50 "
-                            + "absolute_displacement_threshold=3.50 " + "add_tiles_as_rois " + "ignore_z_stage "
+                            + "absolute_displacement_threshold=3.50 " + "add_tiles_as_rois " + "compute_overlap "
                             + "subpixel_accuracy " + "computation_parameters=[Save computation time (but use more RAM)] "
                             + "image_output=[Fuse and display]", this.max_projection_dir, tileconfig.getName()));