Initial commit

Author: Aris-K

.DS_Store

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+# Auto detect text files and perform LF normalization
+* text=auto

.gitattributes

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+//
+// Created by Stephanos Tsoucas on 7/5/17.
+//
+
+#ifndef BOOSTPYTHONHELLOWORLD_ANNOTATION_H
+#define BOOSTPYTHONHELLOWORLD_ANNOTATION_H
+
+#include <armadillo>
+
+using namespace arma;
+
+class Annotation {
+
+  const vec bins;
+  const vec domains;
+  const mat &bin_data;
+  const std::vector<std::pair<uword, uword>> anno;
+
+public:
+  Annotation(vec bin_state_distributions, vec domain_state_distributions,
+             const mat &bin_data,
+             const std::vector<std::pair<uword, uword>> &annotation_data)
+      : bins(bin_state_distributions), domains(domain_state_distributions),
+        bin_data(bin_data), anno(annotation_data) {}
+
+  const vec bin_state_coverage() const { return bins; }
+
+  const vec domain_state_coverage() const { return domains; }
+
+  const std::vector<std::pair<uword, uword>> &annotations() const {
+    return anno;
+  }
+};
+
+#endif // BOOSTPYTHONHELLOWORLD_ANNOTATION_H

Annotation.h

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+//
+// Created by Stephanos Tsoucas on 7/5/17.
+//
+
+#ifndef BOOSTPYTHONHELLOWORLD_ANNOTATION_PY_H
+#define BOOSTPYTHONHELLOWORLD_ANNOTATION_PY_H
+
+#include "Annotation.h"
+#include "Arma_Numpy_Conversions.h"
+
+class Annotation_Py {
+
+  const Annotation a;
+
+public:
+  Annotation_Py(const Annotation annotation) : a(annotation) {}
+
+  np::ndarray bin_state_distributions() {
+    return from_vec(a.bin_state_coverage());
+  }
+
+  np::ndarray domain_state_distributions() {
+    return from_vec(a.domain_state_coverage());
+  }
+
+  np::ndarray annotations() const { return from_vec_of_pairs(a.annotations()); }
+};
+
+#endif // BOOSTPYTHONHELLOWORLD_ANNOTATION_PY_H

Annotation_Py.h

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+//
+// Created by Stephanos Tsoucas on 6/14/17.
+//
+
+#ifndef BOOSTPYTHONHELLOWORLD_ARMA_NUMPY_CONVERSIONS_H
+#define BOOSTPYTHONHELLOWORLD_ARMA_NUMPY_CONVERSIONS_H
+
+#include <armadillo>
+#include <boost/python.hpp>
+#include <boost/python/numpy.hpp>
+
+namespace p = boost::python;
+namespace np = boost::python::numpy;
+namespace a = arma;
+
+np::ndarray from_vec(const a::vec &v) {
+  p::tuple shape = p::make_tuple(v.size());
+  np::dtype dtype = np::dtype::get_builtin<double>();
+  np::ndarray n = np::zeros(shape, dtype);
+
+  for (int i = 0; i < v.size(); i++) {
+    n[i] = v(i);
+  }
+
+  return n;
+}
+
+np::ndarray from_mat(const a::mat &m) {
+  p::tuple shape = p::make_tuple(m.n_rows, m.n_cols);
+  np::dtype dtype = np::dtype::get_builtin<double>();
+  np::ndarray n = np::zeros(shape, dtype);
+
+  for (int i = 0; i < m.n_rows; i++) {
+    for (int j = 0; j < m.n_cols; j++) {
+      n[i][j] = m(i, j);
+    }
+  }
+  return n;
+}
+
+np::ndarray from_cube(const a::cube &c) {
+  p::tuple shape = p::make_tuple(c.n_slices, c.n_rows, c.n_cols);
+  np::dtype dtype = np::dtype::get_builtin<double>();
+  np::ndarray n = np::zeros(shape, dtype);
+
+  for (int slice = 0; slice < c.n_slices; slice++) {
+    for (int i = 0; i < c.n_rows; i++) {
+      for (int j = 0; j < c.n_cols; j++) {
+        n[slice][i][j] = c(i, j, slice);
+      }
+    }
+  }
+
+  return n;
+}
+
+np::ndarray
+from_vec_of_pairs(const std::vector<std::pair<a::uword, a::uword>> &v) {
+  p::tuple shape = p::make_tuple(v.size(), 2);
+  np::dtype dtype = np::dtype::get_builtin<int>();
+  np::ndarray n = np::zeros(shape, dtype);
+
+  for (int i = 0; i < v.size(); i++) {
+    n[i][0] = v.at(i).first;
+    n[i][1] = v.at(i).second;
+  }
+
+  return n;
+}
+
+#endif // BOOSTPYTHONHELLOWORLD_ARMA_NUMPY_CONVERSIONS_H