From aafe95583dd1464aa6069de07a09bd6b423bf644 Mon Sep 17 00:00:00 2001
From: Samuel Fadel <samuelfadel@gmail.com>
Date: Wed, 31 Aug 2016 09:48:24 -0300
Subject: Removed labels handling and bundling when selecting regular points.

---
 main.cpp | 29 +++++++++++++++++++++++------
 main.h   | 13 +++++++------
 2 files changed, 30 insertions(+), 12 deletions(-)

diff --git a/main.cpp b/main.cpp
index 8cc9323..5f7693d 100644
--- a/main.cpp
+++ b/main.cpp
@@ -43,6 +43,18 @@ arma::uvec extractCPs(const arma::mat &X)
     return indices.subvec(0, numCPs-1);
 }
 
+arma::mat standardize(const arma::mat &X)
+{
+    arma::mat stdX = X;
+    for (arma::uword j = 0; j < X.n_cols; j++) {
+        double sd = arma::stddev(stdX.col(j));
+        double mean = arma::mean(stdX.col(j));
+        stdX.col(j) = (stdX.col(j) - mean) / sd;
+    }
+
+    return stdX;
+}
+
 void overviewBundles(const Main *m)
 {
     const arma::mat &unreliability = m->projectionHistory->unreliability();
@@ -105,8 +117,7 @@ int main(int argc, char **argv)
         return 1;
     }
 
-    const arma::mat &X = m->X();
-    //arma::vec labels = m->labels();
+    const arma::mat &X = standardize(m->X());
 
     arma::arma_rng::set_seed(RNG_SEED);
     arma::uvec cpIndices;
@@ -121,6 +132,7 @@ int main(int argc, char **argv)
     if (indicesFile.exists()) {
         m->setIndicesSavePath(indicesFilename);
         cpIndices.load(indicesFilename.toStdString(), arma::raw_ascii);
+        cpIndices -= 1;
     } else {
         std::cerr << "No indices file, generating indices...\n";
         cpIndices = extractCPs(X);
@@ -147,6 +159,10 @@ int main(int argc, char **argv)
         return 1;
     }
 
+    // TODO: maybe put this inside m->setCP() method; for now, will be outside
+    // for more flexibility
+    Ys = arma::normalise(Ys);
+
     // Sort indices (some operations become easier later)
     arma::uvec cpSortedIndices = arma::sort_index(cpIndices);
     cpIndices = cpIndices(cpSortedIndices);
@@ -262,7 +278,7 @@ int main(int argc, char **argv)
                 // Only the 10% largest values, filtered by the selected RPs
                 const arma::mat &unreliability = m->projectionHistory->unreliability();
                 arma::uvec indicesLargest = arma::sort_index(unreliability.cols(selectedCPs), "descending");
-                arma::uword numLargest = indicesLargest.n_elem * 0.1f;
+                arma::uword numLargest = indicesLargest.n_elem * 0.01f;
                 indicesLargest = indicesLargest.subvec(0, numLargest-1);
                 m->bundlePlot->setValues(unreliability(indicesLargest));
 
@@ -293,7 +309,8 @@ int main(int argc, char **argv)
             m->rpPlot, &Scatterplot::setSelection);
     QObject::connect(&rpSelectionHandler, &SelectionHandler::selectionChanged,
             m->rpBarChart, &BarChart::setSelection);
-    QObject::connect(&rpSelectionHandler, &SelectionHandler::selectionChanged,
+    // This still needs more tests
+    /*QObject::connect(&rpSelectionHandler, &SelectionHandler::selectionChanged,
             [m](const std::vector<bool> &rpSelection) {
                 // given some RPs, see unexpected CPs *influencing* them
                 std::vector<arma::uword> selectedRPIndices;
@@ -315,7 +332,7 @@ int main(int argc, char **argv)
                 // Only the 10% largest values, filtered by the selected RPs
                 const arma::mat &unreliability = m->projectionHistory->unreliability();
                 arma::uvec indicesLargest = arma::sort_index(unreliability.rows(selectedRPs), "descending");
-                arma::uword numLargest = indicesLargest.n_elem * 0.1f;
+                arma::uword numLargest = indicesLargest.n_elem * 0.01f;
                 indicesLargest = indicesLargest.subvec(0, numLargest-1);
                 m->bundlePlot->setValues(unreliability(indicesLargest));
 
@@ -335,7 +352,7 @@ int main(int argc, char **argv)
                     indices[2*i + 1] = RPs(i);
                 }
                 m->bundlePlot->setLines(indices, m->projectionHistory->Y());
-            });
+            });*/
 
     // Brushing between each bar chart and respective scatterplot
     BrushingHandler cpBrushHandler;
diff --git a/main.h b/main.h
index 143d49e..9e7ca52 100644
--- a/main.h
+++ b/main.h
@@ -44,7 +44,9 @@ public:
         return ret;
     }
 
-    Q_INVOKABLE bool loadDataset(const std::string &path) { return m_dataset.load(path, arma::raw_ascii); }
+    Q_INVOKABLE bool loadDataset(const std::string &dataPath) {
+        return m_X.load(dataPath, arma::raw_ascii);
+    }
 
     Q_INVOKABLE void setIndicesSavePath(const std::string &path) {
         m_indicesSavePath = path;
@@ -59,8 +61,7 @@ public:
         setCPSavePath(path.toStdString());
     }
 
-    arma::mat X() const { return m_dataset.cols(0, m_dataset.n_cols - 2); }
-    arma::vec labels() const { return m_dataset.col(m_dataset.n_cols - 1); }
+    arma::mat X() const { return m_X; }
 
     Q_INVOKABLE void setSelectRPs() {
         cpPlot->setAcceptedMouseButtons(Qt::NoButton);
@@ -158,8 +159,8 @@ public slots:
     void setCPIndices(const arma::uvec &indices) {
         m_cpIndices = indices;
 
-        m_rpIndices.set_size(m_dataset.n_rows - m_cpIndices.n_elem);
-        NumericRange<arma::uword> allIndices(0, m_dataset.n_rows);
+        m_rpIndices.set_size(m_X.n_rows - m_cpIndices.n_elem);
+        NumericRange<arma::uword> allIndices(0, m_X.n_rows);
         std::set_symmetric_difference(allIndices.cbegin(), allIndices.cend(),
                 m_cpIndices.cbegin(), m_cpIndices.cend(), m_rpIndices.begin());
     }
@@ -220,7 +221,7 @@ private:
         }
     }
 
-    arma::mat m_dataset, m_cp;
+    arma::mat m_X, m_cp;
     arma::uvec m_cpIndices, m_rpIndices;
     std::string m_indicesSavePath, m_cpSavePath;
 };
-- 
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