From e25d0f98506b6627f8db74b23ea0075afa1010cf Mon Sep 17 00:00:00 2001
From: Lisa Tiberio <ltiberio@gmail.com>
Date: Mon, 20 Nov 2017 14:25:04 -0500
Subject: [PATCH 1/4] Created a test wrapper for serialized output. Added the
 call to batch_template.

---
 template_analysis/batch_template.m       |  2 ++
 template_analysis/serializeBatchOutput.m | 38 ++++++++++++++++++++++++
 2 files changed, 40 insertions(+)
 create mode 100644 template_analysis/serializeBatchOutput.m

diff --git a/template_analysis/batch_template.m b/template_analysis/batch_template.m
index fdcefc7..7855344 100644
--- a/template_analysis/batch_template.m
+++ b/template_analysis/batch_template.m
@@ -52,6 +52,8 @@
 OS.FixedInputAxis = [1e4 1e10];
 plot_batch_histograms(results,sampleresults,OS,{'b','y','r'},CM);
 
+[statisticsFile, histogramFile] = serializeBatchOutput(file_pairs, CM, AP, sampleresults, '../');
+
 save('LacI-CAGop-batch.mat','AP','bins','file_pairs','OS','results','sampleresults');
 
 % Dump CSV files:
diff --git a/template_analysis/serializeBatchOutput.m b/template_analysis/serializeBatchOutput.m
new file mode 100644
index 0000000..e2eefd3
--- /dev/null
+++ b/template_analysis/serializeBatchOutput.m
@@ -0,0 +1,38 @@
+% Copyright (C) 2010-2017, Raytheon BBN Technologies and contributors listed
+% in the AUTHORS file in TASBE analytics package distribution's top directory.
+%
+% This file is part of the TASBE analytics package, and is distributed
+% under the terms of the GNU General Public License, with a linking
+% exception, as described in the file LICENSE in the TASBE analytics
+% package distribution's top directory.
+
+function [statisticsFile, histogramFile] = serializeBatchOutput(file_pairs, CM, AP, sampleresults, pathToOutputFiles)
+
+    % Grab all the data in separate data structures. Then format for output
+    % files.
+    numConditions = size(file_pairs,1);
+    histogramFile = [pathToOutputFiles '/histogramFile.csv'];
+    
+    channels = getChannels(CM);
+    sampleIds = file_pairs(:,1);
+    binCenters = get_bin_centers(getBins(AP));
+    
+    for i=1:numConditions
+        binCounts{i} = sampleresults{i}{1}.BinCounts;
+        geoMeans{i} = sampleresults{i}{1}.Means;
+        geoStdDev{i} = sampleresults{i}{1}.StandardDevs;
+    end
+    
+    % Formats and writes the output to the Statistics file.
+    statisticsFile = writeStatisticsCsv(numConditions, channels, sampleIds, binCounts, geoMeans, geoStdDev, pathToOutputFiles);
+    
+    % Formats and writes the output to the Histogram file.
+    %histogramFile = writeHistogramCsv(numConditions, channels, sampleIds, binCounts, binCenters, pathToOutputFiles);
+    
+    % Write the data points to a file (without headers for now). This is 
+    %  just a wrapper around readfcs_compensated_ERF. It returns
+    % the data, but for now ignore it because I'm testing writing files.
+    %fcsToCsvFlowConverterFileWriter(CM, filename, getUseAutoFluorescence(AP), floor);
+
+end
+

From 73605e5df955d31d567d9c4ada906d7b112f9a5c Mon Sep 17 00:00:00 2001
From: Lisa Tiberio <ltiberio@gmail.com>
Date: Wed, 29 Nov 2017 13:48:57 -0500
Subject: [PATCH 2/4] Unit test code.

---
 template_analysis/serializeBatchOutput.m |   2 +-
 template_colormodel/CM120312-Lisa.mat    | Bin 0 -> 7424 bytes
 2 files changed, 1 insertion(+), 1 deletion(-)
 create mode 100644 template_colormodel/CM120312-Lisa.mat

diff --git a/template_analysis/serializeBatchOutput.m b/template_analysis/serializeBatchOutput.m
index e2eefd3..5a6a869 100644
--- a/template_analysis/serializeBatchOutput.m
+++ b/template_analysis/serializeBatchOutput.m
@@ -27,7 +27,7 @@
     statisticsFile = writeStatisticsCsv(numConditions, channels, sampleIds, binCounts, geoMeans, geoStdDev, pathToOutputFiles);
     
     % Formats and writes the output to the Histogram file.
-    %histogramFile = writeHistogramCsv(numConditions, channels, sampleIds, binCounts, binCenters, pathToOutputFiles);
+    histogramFile = writeHistogramCsv(numConditions, channels, sampleIds, binCounts, binCenters, pathToOutputFiles);
     
     % Write the data points to a file (without headers for now). This is 
     %  just a wrapper around readfcs_compensated_ERF. It returns
diff --git a/template_colormodel/CM120312-Lisa.mat b/template_colormodel/CM120312-Lisa.mat
new file mode 100644
index 0000000000000000000000000000000000000000..b7f16fa6a5838fe05ebc67e0c95a873b11e8f7cd
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From 58a3955fb8431ec9b307b6750d36d9e65555a936 Mon Sep 17 00:00:00 2001
From: ltiberio <lisa.tiberio@gmail.com>
Date: Tue, 19 Dec 2017 16:16:53 -0500
Subject: [PATCH 3/4] Moved this file into the TASBE code directory.

---
 template_analysis/serializeBatchOutput.m | 38 ------------------------
 1 file changed, 38 deletions(-)
 delete mode 100644 template_analysis/serializeBatchOutput.m

diff --git a/template_analysis/serializeBatchOutput.m b/template_analysis/serializeBatchOutput.m
deleted file mode 100644
index 5a6a869..0000000
--- a/template_analysis/serializeBatchOutput.m
+++ /dev/null
@@ -1,38 +0,0 @@
-% Copyright (C) 2010-2017, Raytheon BBN Technologies and contributors listed
-% in the AUTHORS file in TASBE analytics package distribution's top directory.
-%
-% This file is part of the TASBE analytics package, and is distributed
-% under the terms of the GNU General Public License, with a linking
-% exception, as described in the file LICENSE in the TASBE analytics
-% package distribution's top directory.
-
-function [statisticsFile, histogramFile] = serializeBatchOutput(file_pairs, CM, AP, sampleresults, pathToOutputFiles)
-
-    % Grab all the data in separate data structures. Then format for output
-    % files.
-    numConditions = size(file_pairs,1);
-    histogramFile = [pathToOutputFiles '/histogramFile.csv'];
-    
-    channels = getChannels(CM);
-    sampleIds = file_pairs(:,1);
-    binCenters = get_bin_centers(getBins(AP));
-    
-    for i=1:numConditions
-        binCounts{i} = sampleresults{i}{1}.BinCounts;
-        geoMeans{i} = sampleresults{i}{1}.Means;
-        geoStdDev{i} = sampleresults{i}{1}.StandardDevs;
-    end
-    
-    % Formats and writes the output to the Statistics file.
-    statisticsFile = writeStatisticsCsv(numConditions, channels, sampleIds, binCounts, geoMeans, geoStdDev, pathToOutputFiles);
-    
-    % Formats and writes the output to the Histogram file.
-    histogramFile = writeHistogramCsv(numConditions, channels, sampleIds, binCounts, binCenters, pathToOutputFiles);
-    
-    % Write the data points to a file (without headers for now). This is 
-    %  just a wrapper around readfcs_compensated_ERF. It returns
-    % the data, but for now ignore it because I'm testing writing files.
-    %fcsToCsvFlowConverterFileWriter(CM, filename, getUseAutoFluorescence(AP), floor);
-
-end
-

From cfa4c322cf03ebfdbbf8167cbc42686a95da9659 Mon Sep 17 00:00:00 2001
From: jakebeal <jakebeal@alum.mit.edu>
Date: Wed, 17 Jan 2018 18:33:08 -0600
Subject: [PATCH 4/4] testing color models shouldn't have been included

---
 template_colormodel/CM120312-Lisa.mat | Bin 7424 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 template_colormodel/CM120312-Lisa.mat

diff --git a/template_colormodel/CM120312-Lisa.mat b/template_colormodel/CM120312-Lisa.mat
deleted file mode 100644
index b7f16fa6a5838fe05ebc67e0c95a873b11e8f7cd..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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