From 070f91a4edc5005259bad55f2d12111e4544f3c5 Mon Sep 17 00:00:00 2001
From: Antonin Portelli <antonin.portelli@me.com>
Date: Thu, 4 Apr 2019 20:05:23 +0100
Subject: [PATCH] correlation matrix plot utility can (optionally) save
 matrices

---
 utils/sample-plot-corr.cpp | 41 +++++++++++++++++++++++++++++++++-----
 1 file changed, 36 insertions(+), 5 deletions(-)

diff --git a/utils/sample-plot-corr.cpp b/utils/sample-plot-corr.cpp
index 47af749..2a1e260 100644
--- a/utils/sample-plot-corr.cpp
+++ b/utils/sample-plot-corr.cpp
@@ -17,6 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include <LatAnalyze/Core/OptParser.hpp>
 #include <LatAnalyze/Io/Io.hpp>
 #include <LatAnalyze/Core/Math.hpp>
 #include <LatAnalyze/Core/Plot.hpp>
@@ -27,16 +28,37 @@ using namespace Math;
 
 int main(int argc, char *argv[])
 {
-    if (argc != 2)
+    OptParser      opt;
+    bool           parsed;
+    string         outCorrName = "", outVarName = "";
+
+    opt.addOption("", "saveCorr", OptParser::OptType::value, true,
+                  "save correlation matrix (default: not saved)");
+    opt.addOption("", "saveVar", OptParser::OptType::value, true,
+                  "save variance matrix (default: not saved)");
+    opt.addOption("" , "help"  , OptParser::OptType::trigger, true,
+                  "show this help message and exit");
+    parsed = opt.parse(argc, argv);
+    if (!parsed or (opt.getArgs().size() != 1) or opt.gotOption("help"))
     {
-        cerr << "usage: " << argv[0] << " <file>" << endl;
+        cerr << "usage: " << argv[0];
+        cerr << "<options> <sample file>" << endl;
+        cerr << endl << "Possible options:" << endl << opt << endl;
         
         return EXIT_FAILURE;
     }
+    if (opt.gotOption("saveCorr"))
+    {
+        outCorrName = opt.optionValue("saveCorr");
+    }
+    if (opt.gotOption("saveVar"))
+    {
+        outVarName = opt.optionValue("saveVar");
+    }
     
-    string     fileName = argv[1], name;
+    string     fileName = opt.getArgs()[0], name;
     DMatSample sample;
-    DMat       var;
+    DMat       var, corr;
     Plot       p;
     
     cout << "-- computing variance matrix from '" << fileName << "'..." << endl;
@@ -44,8 +66,17 @@ int main(int argc, char *argv[])
     sample = Io::load<DMatSample>(fileName);
     sample = sample.block(0, 0, sample[central].rows(), 1);
     var    = sample.varianceMatrix();
-    p << PlotMatrix(varToCorr(var));
+    corr   = sample.correlationMatrix();
+    p << PlotMatrix(corr);
     p.display();
+    if (!outVarName.empty())
+    {
+        Io::save(var, outVarName);
+    }
+    if (!outCorrName.empty())
+    {
+        Io::save(corr, outCorrName);
+    }
     
     return EXIT_SUCCESS;
 }