From c49d196e3a4a1f131ef82602a79db057903bc974 Mon Sep 17 00:00:00 2001
From: Florian Vollrath <florian.vollrath@brain.mpg.de>
Date: Tue, 24 Apr 2018 08:37:03 +0200
Subject: [PATCH] added a script for import, alignement and export of stack
 data

---
 realignementScript.m | 50 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 realignementScript.m

diff --git a/realignementScript.m b/realignementScript.m
new file mode 100644
index 0000000..890754a
--- /dev/null
+++ b/realignementScript.m
@@ -0,0 +1,50 @@
+%% Paramters
+%input file
+inFileGren = 'D:\data\BelenTestData\Out\complete_g.tif';
+inFileRed = 'D:\data\BelenTestData\Out\complete_g.tif';
+
+%oiutput file
+outFileGreen = 'D:\data\BelenTestData\Out\complete_g_Grealigned.tif';
+outFileRed = 'D:\data\BelenTestData\Out\complete_g_Rrealigned.tif';
+
+%Apply Gaussian Filter before correction?
+bGaussian = 0;
+
+%reference channels
+referenceChannel = 1; %1: red, 0: green
+numShiftCorrections = 1;
+
+nSubIm = 200;%number of subImages for med align
+numImages = 50; %number of images that will be meaned for global shift correction
+%% Load data and perform correction
+data_r = loadtiff(inFileRed);
+data_g = loadtiff(inFileGren);
+
+for j = 1:numShiftCorrections
+    if referenceChannel
+        referenceChannelData = data_r;
+    else
+        referenceChannelData = data_g;
+    end
+    
+    if bGaussian
+        for f=1:size(referenceChannelData,3)
+            referenceChannelData(:,:,f) = imgaussfilt(referenceChannelData(:,:,f),2);
+        end
+    end
+    
+    %Med Align
+    [rs, cs] = medAlign(referenceChannelData, nSubIm, 50, -inf);
+    %shift red and green channel
+    %waitbar(j/numShiftCorrections, wb, 'Performing Med Align..');
+    for i = 1:size(data_g,3)
+        data_r(:,:,i) = circshift(data_r(:,:,i),[rs(i),cs(i)]);
+        data_g(:,:,i) = circshift(data_g(:,:,i),[rs(i),cs(i)]);
+    end
+end
+
+%% Exort Data
+
+saveastiff(data_r, outFileRed);
+saveastiff(data_g, outFileGreen);
+