From 3e33e88cb3521c845c8fae1dcf5a43a6a19f28a1 Mon Sep 17 00:00:00 2001
From: dcluet <david.cluet@ens-lyon.fr>
Date: Tue, 2 Oct 2018 10:31:40 +0200
Subject: [PATCH] Add choice for a contrast channel

---
 src/Macro/Lipid_Droplets.java |  5 +++--
 src/Macro/Select_Channel.java | 11 ++++++++---
 src/Macro/Taylor.java         | 12 +++++++-----
 3 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/src/Macro/Lipid_Droplets.java b/src/Macro/Lipid_Droplets.java
index 96eea2d..f7bfb6b 100644
--- a/src/Macro/Lipid_Droplets.java
+++ b/src/Macro/Lipid_Droplets.java
@@ -95,7 +95,8 @@ FP = Arguments[23];
 minimumFound = parseFloat(Arguments[24]);
 
 //Channel to be treated
-channel = Arguments[25];
+channels = split(Arguments[25], ";");
+channel = channels[0];
 
 /*
 ============================================================================
@@ -1032,7 +1033,7 @@ function UpdateMD(MD){
                         FolderOutputRelative + NameFile + "_Intensities_Non-NP_Cumul_Distribution.jpg");
 
     for (index=0; index<myKeywords.length; index++){
-        MD = replace(MD, myKeywords[index], myValues[index]);        
+        MD = replace(MD, myKeywords[index], myValues[index]);
     }
     return MD;
 }
diff --git a/src/Macro/Select_Channel.java b/src/Macro/Select_Channel.java
index 8ff812f..fecfb75 100644
--- a/src/Macro/Select_Channel.java
+++ b/src/Macro/Select_Channel.java
@@ -69,14 +69,19 @@ macro "Select_Channel.java"{
 
             //Attribute the channel for analysis
             Dialog.create("Choose the channel to use.");
-            Dialog.addChoice("Channels: ",
+            Dialog.addChoice("Main channel: ",
                             channelsNames,
                             channelsNames[0]);
+            Dialog.addChoice("Contrast channel: ",
+                            channelsNames,
+                            channelsNames[1]);
             Dialog.show();
-            myChannel = Dialog.getChoice();
+            myChannel1 = Dialog.getChoice();
+            myChannel2 = Dialog.getChoice();
+            myChannel = myChannel1 + ";" + myChannel2;
 
         }else{
-            myChannel = "C0-";
+            myChannel = "C0-;C0-";
         }
 
         //Close all non required images.
diff --git a/src/Macro/Taylor.java b/src/Macro/Taylor.java
index 70ca83f..1738652 100644
--- a/src/Macro/Taylor.java
+++ b/src/Macro/Taylor.java
@@ -29,7 +29,9 @@ macro "Taylor"{
     minNew = parseFloat(Arguments[7]);
 
     //Channel to treat
-    myChannel = Arguments[8];
+    channels = split(Arguments[8], ";");
+    myChannel = channels[0];
+    myChannelContrast = channels[1];
 
     //Common parameters for all stacks
     ARGcommon = Arguments[9];
@@ -122,8 +124,8 @@ function ClassicalSetUp(){
             run("Split Channels");
 
             //Attribute LUT to increase display resoltion
-            Bodipy = "C1-" + Titre;
-            Tissue = "C2-" + Titre;
+            Bodipy = myChannel + Titre;
+            Tissue = myChannelContrast + Titre;
             selectWindow(Bodipy);
             run("Enhance Contrast", "saturated=0.35");
             run("Green");
@@ -211,7 +213,7 @@ function ClassicalSetUp(){
         ARG += "" + (myFile/nFiles) + "*";
         ARG += "" + FPT + "*" + FP + "*";
         ARG += "" + minNew + "*";
-        ARG += "" + myChannel;
+        ARG += "" + myChannel + ";" + myChannelContrast;
 
         //Update the command file
         File.append(ARG, myCommands);
@@ -279,7 +281,7 @@ function RecycleSetUp(){
         ARG += "" + myProgress + "*";
         ARG += "" + FPT + "*" + FP + "*";
         ARG += "" + minNew + "*";
-        ARG += "" + myChannel;
+        ARG += "" + myChannel + ";" + myChannelContrast;
 
         //Update the command file
         File.append(ARG, myCommands);
-- 
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