From a4d8d04931650c77146173d3e4c37c9c6f093267 Mon Sep 17 00:00:00 2001
From: Florian Vollrath <florian.vollrath@brain.mpg.de>
Date: Sun, 9 Oct 2016 22:43:19 +0200
Subject: [PATCH] fixed stuff

---
 functions/CellSortLoadTrials.m                  | 13 +++++++++++++
 functions/CellSortLoadTrialsShiftCorrOnTrials.m |  2 +-
 main.m                                          |  2 ++
 3 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/functions/CellSortLoadTrials.m b/functions/CellSortLoadTrials.m
index 12f32e1..31d731c 100644
--- a/functions/CellSortLoadTrials.m
+++ b/functions/CellSortLoadTrials.m
@@ -46,5 +46,18 @@
 %do shift correction on complete video
 disp('Performing Shift Correction On All Frames..');
 [data_g_array, data_r_array] = CellSortShiftCorrection(data_g_array,data_r_array,reference, 'iter');
+
+%calculate quality plot
+reference = mean(data_r_array, 3);
+qualityPlot = zeros(1,size(data_r_array, 3));
+parfor i = 1:size(data_r_array,3)
+    qualityPlot(i) = squeeze(mean(mean(data_r_array(:,:,i) - reference,1),2));
+end
+qualityPlot = qualityPlot.^2;
+figure;
+plot(qualityPlot);
+for i=1:numberGreen
+    vline(numFrameList(i), 'black', greenFiles(i).name);
+end
 disp('Finished Loading Trial Files!');
 end
\ No newline at end of file
diff --git a/functions/CellSortLoadTrialsShiftCorrOnTrials.m b/functions/CellSortLoadTrialsShiftCorrOnTrials.m
index 836fc87..b548146 100644
--- a/functions/CellSortLoadTrialsShiftCorrOnTrials.m
+++ b/functions/CellSortLoadTrialsShiftCorrOnTrials.m
@@ -50,7 +50,6 @@
     data_g{i} = [];
 end
 
-disp('Finished Loading Trial Files!');
 %calculate quality plot
 reference = mean(data_r_array, 3);
 qualityPlot = zeros(1,size(data_r_array, 3));
@@ -63,4 +62,5 @@
 for i=1:numberGreen
     vline(numFrameList(i), 'black', greenFiles(i).name);
 end
+disp('Finished Loading Trial Files!');
 end
\ No newline at end of file
diff --git a/main.m b/main.m
index 1ace0e6..a29b2b5 100644
--- a/main.m
+++ b/main.m
@@ -12,7 +12,9 @@
 %% load files
 %go to corr folder
 outFolder = 'F:\Arbeit\testData\PCAICA';
+%shifft correction on all frames
 %[data_g, data_r, frames, fn_green, fn_red, fileNamesGreen, fileNamesRed] = CellSortLoadTrials(outFolder);
+%shift correction only on trials
 [data_g, data_r, frames, fn_green, fn_red, fileNamesGreen, fileNamesRed] = CellSortLoadTrialsShiftCorrOnTrials(outFolder);
 %If you want to load single files, use the functions below.
 % fn_green = 'data_g.tif';