Initial import.

LICENSE

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+The MIT License
+
+Copyright (c) 2009 Indiana University
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

Makefile

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+objects = \
+	binary_matrix.o \
+	binary_vector.o \
+	degrees_dir.o \
+	degrees_und.o \
+	matrix_printf.o \
+	vector_printf.o
+bct: $(objects)
+	libtool -static -o libbct.a $(objects)
+binary_matrix.o:
+	cc -c binary_matrix.cpp
+binary_vector.o:
+	cc -c binary_vector.cpp
+degrees_dir.o:
+	cc -c degrees_dir.cpp
+degrees_und.o:
+	cc -c degrees_und.cpp
+matrix_printf.o:
+	cc -c matrix_printf.cpp
+vector_printf.o:
+	cc -c vector_printf.cpp
+clean:
+	-rm libbct.a $(objects)

README

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+bct-cpp is a C++ port of the Brain Connectivity Toolbox, a set of MATLAB
+functions and neuroanatomical data sets useful in the analysis of structural
+or functional brain networks.
+
+See <http://www.brain-connectivity-toolbox.net/> for more information.
+
+See LICENSE for information about bct-cpp's license.

bct.h

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+#ifndef BCT_H
+#define BCT_H
+
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_vector.h>
+
+namespace bct {
+	const double EPSILON = 1e-6;  // Used for floating-point equality comparisons
+
+	// Density, degree, and assortativity
+	gsl_vector* degrees_und(const gsl_matrix*);
+	gsl_vector* degrees_dir_in(const gsl_matrix*);
+	gsl_vector* degrees_dir_out(const gsl_matrix*);
+	gsl_vector* degrees_dir(const gsl_matrix*);
+
+	// Clustering
+
+	// Paths, distances, and cycles
+
+	// Centrality
+
+	// Motifs
+
+	// Modularity and community structure
+
+	// Utility
+	gsl_vector* binary_vector(const gsl_vector*);
+	gsl_matrix* binary_matrix(const gsl_matrix*);
+
+	// Debugging
+	void vector_printf(const gsl_vector*, const char*);
+	void matrix_printf(const gsl_matrix*, const char*);
+};
+
+#endif

binary_matrix.cpp

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+#include "bct.h"
+#include <gsl/gsl_matrix.h>
+
+/*
+ * Returns a binary copy of the given matrix.
+ */
+gsl_matrix* bct::binary_matrix(const gsl_matrix* m) {
+	gsl_matrix* bm = gsl_matrix_calloc(m->size1, m->size2);
+	for (int i = 0; i < m->size1; i++) {
+		for (int j = 0; j < m->size2; j++) {
+			if (abs(gsl_matrix_get(m, i, j)) > EPSILON) {
+				gsl_matrix_set(bm, i, j, 1.0);
+			}
+		}
+	}
+	return bm;
+}

binary_vector.cpp

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+#include "bct.h"
+#include <gsl/gsl_vector.h>
+
+/*
+ * Returns a binary copy of the given vector.
+ */
+gsl_vector* bct::binary_vector(const gsl_vector* v) {
+	gsl_vector* bv = gsl_vector_calloc(v->size);
+	for (int i = 0; i < v->size; i++) {
+		if (abs(gsl_vector_get(v, i)) > EPSILON) {
+			gsl_vector_set(bv, i, 1.0);
+		}
+	}
+	return bv;
+}

degrees_dir.cpp

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+#include "bct.h"
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_vector.h>
+
+/*
+ * Computes the in-degree for each node in a directed binary matrix.  Weights
+ * are discarded.  Results are returned in a vector where each element is the
+ * in-degree of the corresponding node.
+ */
+gsl_vector* bct::degrees_dir_in(const gsl_matrix* m) {
+
+	// Calculated the same way as degrees_und
+	return degrees_und(m);
+}
+
+/*
+ * Computes the out-degree for each node in a directed binary matrix.  Weights
+ * are discarded.  Results are returned in a vector where each element is the
+ * out-degree of the corresponding node.
+ */
+gsl_vector* bct::degrees_dir_out(const gsl_matrix* m) {
+	gsl_matrix* bm = binary_matrix(m);
+	gsl_vector* out_degrees = gsl_vector_calloc(bm->size1);
+	for (int i = 0; i < bm->size2; i++) {
+		gsl_vector_const_view column = gsl_matrix_const_column(bm, i);
+		gsl_vector_add(out_degrees, &column.vector);
+	}
+	gsl_matrix_free(bm);
+	return out_degrees;
+}
+
+/*
+ * Computes the degree for each node in a directed binary matrix.  Weights are
+ * discarded.  Results are returned in a vector where each element is the degree
+ * of the corresponding node.
+ */
+gsl_vector* bct::degrees_dir(const gsl_matrix* m) {
+	gsl_vector* in_degrees = degrees_dir_in(m);
+	gsl_vector* out_degrees = degrees_dir_out(m);
+	gsl_vector_add(in_degrees, out_degrees);
+	gsl_vector_free(out_degrees);
+	return in_degrees;
+}

degrees_und.cpp

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+#include "bct.h"
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_vector.h>
+
+/*
+ * Computes the degree for each node in an undirected binary matrix.  Weights
+ * are discarded.  Results are returned in a vector where each element is the
+ * degree of the corresponding node.
+ */
+gsl_vector* bct::degrees_und(const gsl_matrix* m) {
+	gsl_matrix* bm = binary_matrix(m);
+	gsl_vector* degrees = gsl_vector_calloc(bm->size2);
+	for (int i = 0; i < bm->size1; i++) {
+		gsl_vector_const_view row = gsl_matrix_const_row(bm, i);
+		gsl_vector_add(degrees, &row.vector);
+	}
+	gsl_matrix_free(bm);
+	return degrees;
+}

matrix_printf.cpp

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+#include "bct.h"
+#include <cstdio>
+#include <gsl/gsl_matrix.h>
+
+/*
+ * Prints a matrix using the given format for each element.  This is only
+ * provided for debugging purposes.  In other cases, use gsl_matrix_fprintf.
+ */
+void bct::matrix_printf(const gsl_matrix* m, const char* format) {
+	for (int i = 0; i < m->size1; i++) {
+		for (int j = 0; j < m->size2; j++) {
+			std::printf(format, gsl_matrix_get(m, i, j));
+			std::printf(" ");
+		}
+		std::printf("\n");
+	}
+}

vector_printf.cpp

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+#include "bct.h"
+#include <cstdio>
+#include <gsl/gsl_vector.h>
+
+/*
+ * Prints a vector using the given format for each element.  This is only
+ * provided for debugging purposes.  In other cases, use gsl_vector_fprintf.
+ */
+void bct::vector_printf(const gsl_vector* v, const char* format) {
+	for (int i = 0; i < v->size; i++) {
+		std::printf(format, gsl_vector_get(v, i));
+		std::printf(" ");
+	}
+	std::printf("\n");
+}