diff --git a/.gitignore b/.gitignore
index 234bd3c4550c07f52be5458bc10ea92d4019b870..c23dfde0164c2ce71be3a2113f47b2f96e793753 100644
--- a/.gitignore
+++ b/.gitignore
@@ -41,3 +41,9 @@
*.toc
*.blg
+# cmake
+CMakeFiles
+CMakeCache.txt
+cmake_install.cmake
+Makefile
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..717eb124c4eb1e08d455bdf73446fabec96a6265
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,21 @@
+cmake_minimum_required (VERSION 2.8)
+
+# project info
+project (cell_algorithms)
+enable_language(CXX)
+
+# compilation flags
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -pthread -Wall")
+
+# this generates a .json file with full compilation command for each file
+set(CMAKE_EXPORT_COMPILE_COMMANDS "YES")
+
+# generated .a and .so go into /lib
+#set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+#set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+
+include_directories(${CMAKE_SOURCE_DIR}/src)
+include_directories(${CMAKE_SOURCE_DIR})
+
+add_subdirectory(tests)
+
diff --git a/cells_small.json b/data/cells_small.json
similarity index 100%
rename from cells_small.json
rename to data/cells_small.json
diff --git a/makefile b/makefile
deleted file mode 100644
index 736a149f83bcb53f082a9a3656d7f1ef5ca5f321..0000000000000000000000000000000000000000
--- a/makefile
+++ /dev/null
@@ -1,13 +0,0 @@
-CC=clang++
-FLAGS=-std=c++11 -g -pedantic
-
-test.exe : main.cpp *.hpp makefile gtest.o
- $(CC) $(FLAGS) main.cpp -o test.exe gtest.o -pthread
-
-gtest.o :
- $(CC) $(FLAGS) gtest-all.cc -c -o gtest.o
-
-clean :
- rm -f test.exe
- rm -f gtest.o
- rm -f a.out
diff --git a/cell_tree.hpp b/src/cell_tree.hpp
similarity index 99%
rename from cell_tree.hpp
rename to src/cell_tree.hpp
index 3daf48d56620725dae2bb44cb47dfe318b4ab0c5..e6ba5b2e9dcb4c19e1708bf7d87554f47cfb5f94 100644
--- a/cell_tree.hpp
+++ b/src/cell_tree.hpp
@@ -192,7 +192,6 @@ class cell_tree {
auto max = std::max_element(depth.begin(), depth.end());
auto max_leaf = std::distance(depth.begin(), max);
- auto original_depth = *max;
// Calculate the depth of each compartment as the maximum distance
// from a child leaf
diff --git a/swcio.hpp b/src/swcio.hpp
similarity index 100%
rename from swcio.hpp
rename to src/swcio.hpp
diff --git a/tree.hpp b/src/tree.hpp
similarity index 98%
rename from tree.hpp
rename to src/tree.hpp
index 772eb86c99d55ac65b076ee8ab164d1ae0c6c675..04f8ccd4d35b207a5567906d3eb84c47058340c2 100644
--- a/tree.hpp
+++ b/src/tree.hpp
@@ -58,10 +58,6 @@ class tree {
}
}
- // The number of children is the number of branches, excluding the root branch.
- // num_children is equivalent to the number of edges in the graph.
- auto nchildren = nbranches-1;
-
// allocate memory for storing the tree
init(nbranches);
diff --git a/util.hpp b/src/util.hpp
similarity index 98%
rename from util.hpp
rename to src/util.hpp
index d37c7f65427f1bd7e12edc8ee10b0f95fcb47ba8..17a3a49b0a19ee867229f71e08ab27b2c6962d57 100644
--- a/util.hpp
+++ b/src/util.hpp
@@ -2,12 +2,14 @@
#include "vector/include/Vector.hpp"
+/*
using memory::util::red;
using memory::util::yellow;
using memory::util::green;
using memory::util::white;
using memory::util::blue;
using memory::util::cyan;
+*/
#include <ostream>
#include <vector>
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba8b481ad51109f2a758ebd19c4281d5f3792d2f
--- /dev/null
+++ b/tests/CMakeLists.txt
@@ -0,0 +1,27 @@
+set(HEADERS
+ ../src/swcio.hpp
+ ../src/tree.hpp
+ ../src/cell_tree.hpp
+)
+
+set(TEST_SOURCES
+ # google test framework
+ gtest-all.cpp
+
+ # unit tests
+ test_swcio.cpp
+ test_tree.cpp
+
+ # unit test driver
+ main.cpp
+)
+
+add_executable(test.exe ${TEST_SOURCES} ${HEADERS})
+
+#target_link_libraries(test_compiler LINK_PUBLIC compiler gtest)
+
+#set_target_properties( test.exe
+# PROPERTIES
+# RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests"
+#)
+
diff --git a/gtest-all.cc b/tests/gtest-all.cpp
similarity index 99%
rename from gtest-all.cc
rename to tests/gtest-all.cpp
index c3fb36ab25b692ce827eda4ccf8a85fbc3a923ae..641a64833c5b79f930e0206d82b44279f2f1dbe8 100644
--- a/gtest-all.cc
+++ b/tests/gtest-all.cpp
@@ -36,7 +36,7 @@
// This line ensures that gtest.h can be compiled on its own, even
// when it's fused.
-#include "gtest/gtest.h"
+#include "gtest.h"
// The following lines pull in the real gtest *.cc files.
// Copyright 2005, Google Inc.
diff --git a/gtest/gtest.h b/tests/gtest.h
similarity index 100%
rename from gtest/gtest.h
rename to tests/gtest.h
diff --git a/tests/main.cpp b/tests/main.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..f2eab0931a0b4b2a5b17ed12ba6c2f3d1d09d27c
--- /dev/null
+++ b/tests/main.cpp
@@ -0,0 +1,11 @@
+#include <iostream>
+#include <fstream>
+#include <numeric>
+#include <vector>
+
+#include "gtest.h"
+
+int main(int argc, char **argv) {
+ ::testing::InitGoogleTest(&argc, argv);
+ return RUN_ALL_TESTS();
+}
diff --git a/make_image.sh b/tests/make_image.sh
similarity index 100%
rename from make_image.sh
rename to tests/make_image.sh
diff --git a/tests/test_swcio.cpp b/tests/test_swcio.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..862f5a1cc343c62aa0e192e352c188bb22e86f74
--- /dev/null
+++ b/tests/test_swcio.cpp
@@ -0,0 +1,182 @@
+#include <iostream>
+#include <fstream>
+#include <numeric>
+#include <vector>
+
+#include "gtest.h"
+
+#include "swcio.hpp"
+
+// SWC tests
+void expect_cell_equals(const neuron::io::cell_record &expected,
+ const neuron::io::cell_record &actual)
+{
+ EXPECT_EQ(expected.id(), actual.id());
+ EXPECT_EQ(expected.type(), actual.type());
+ EXPECT_FLOAT_EQ(expected.x(), actual.x());
+ EXPECT_FLOAT_EQ(expected.y(), actual.y());
+ EXPECT_FLOAT_EQ(expected.z(), actual.z());
+ EXPECT_FLOAT_EQ(expected.radius(), actual.radius());
+ EXPECT_EQ(expected.parent(), actual.parent());
+}
+
+TEST(cell_record, construction)
+{
+ using namespace neuron::io;
+
+ {
+ // force an invalid type
+ cell_record::kind invalid_type = static_cast<cell_record::kind>(100);
+ EXPECT_THROW(cell_record cell(invalid_type, 7, 1., 1., 1., 1., 5),
+ std::invalid_argument);
+ }
+
+ {
+ // invalid id
+ EXPECT_THROW(cell_record cell(
+ cell_record::custom, -3, 1., 1., 1., 1., 5),
+ std::invalid_argument);
+ }
+
+ {
+ // invalid parent id
+ EXPECT_THROW(cell_record cell(
+ cell_record::custom, 0, 1., 1., 1., 1., -5),
+ std::invalid_argument);
+ }
+
+ {
+ // invalid radius
+ EXPECT_THROW(cell_record cell(
+ cell_record::custom, 0, 1., 1., 1., -1., -1),
+ std::invalid_argument);
+ }
+
+ {
+ // parent_id > id
+ EXPECT_THROW(cell_record cell(
+ cell_record::custom, 0, 1., 1., 1., 1., 2),
+ std::invalid_argument);
+ }
+
+ {
+ // parent_id == id
+ EXPECT_THROW(cell_record cell(
+ cell_record::custom, 0, 1., 1., 1., 1., 0),
+ std::invalid_argument);
+ }
+
+ {
+ // check standard construction by value
+ cell_record cell(cell_record::custom, 0, 1., 1., 1., 1., -1);
+ EXPECT_EQ(cell.id(), 0);
+ EXPECT_EQ(cell.type(), cell_record::custom);
+ EXPECT_EQ(cell.x(), 1.);
+ EXPECT_EQ(cell.y(), 1.);
+ EXPECT_EQ(cell.z(), 1.);
+ EXPECT_EQ(cell.radius(), 1.);
+ EXPECT_EQ(cell.diameter(), 2*1.);
+ EXPECT_EQ(cell.parent(), -1);
+ }
+
+ {
+ // check copy constructor
+ cell_record cell_orig(cell_record::custom, 0, 1., 1., 1., 1., -1);
+ cell_record cell(cell_orig);
+ expect_cell_equals(cell_orig, cell);
+ }
+}
+
+TEST(swc_parser, invalid_input)
+{
+ using namespace neuron::io;
+
+ {
+ // check incomplete lines; missing parent
+ std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830\n");
+ cell_record cell;
+ EXPECT_THROW(is >> cell, std::logic_error);
+ }
+
+ {
+ // Check non-parsable values
+ std::istringstream is("1a 1 14.566132 34.873772 7.857000 0.717830 -1\n");
+ cell_record cell;
+ EXPECT_THROW(is >> cell, std::logic_error);
+ }
+
+ {
+ // Check invalid cell type
+ std::istringstream is("1 10 14.566132 34.873772 7.857000 0.717830 -1\n");
+ cell_record cell;
+ EXPECT_THROW(is >> cell, std::invalid_argument);
+ }
+}
+
+
+TEST(swc_parser, valid_input)
+{
+ using namespace neuron::io;
+
+ {
+ // check empty file; no cell may be parsed
+ cell_record cell, cell_orig;
+ std::istringstream is("");
+ EXPECT_NO_THROW(is >> cell);
+ expect_cell_equals(cell_orig, cell);
+ }
+
+ {
+ // check comment-only file not ending with a newline;
+ // no cell may be parsed
+ cell_record cell, cell_orig;
+ std::istringstream is("#comment\n#comment");
+ EXPECT_NO_THROW(is >> cell);
+ expect_cell_equals(cell_orig, cell);
+ }
+
+
+ {
+ // check last line case (no newline at the end)
+ std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830 -1");
+ cell_record cell;
+ EXPECT_NO_THROW(is >> cell);
+ EXPECT_EQ(0, cell.id()); // zero-based indexing
+ EXPECT_EQ(cell_record::soma, cell.type());
+ EXPECT_FLOAT_EQ(14.566132, cell.x());
+ EXPECT_FLOAT_EQ(34.873772, cell.y());
+ EXPECT_FLOAT_EQ( 7.857000, cell.z());
+ EXPECT_FLOAT_EQ( 0.717830, cell.radius());
+ EXPECT_FLOAT_EQ( -1, cell.parent());
+ }
+
+ {
+ // check valid input with a series of records
+ std::vector<cell_record> cells_orig = {
+ cell_record(cell_record::soma, 0,
+ 14.566132, 34.873772, 7.857000, 0.717830, -1),
+ cell_record(cell_record::dendrite, 1,
+ 14.566132+1, 34.873772+1, 7.857000+1, 0.717830+1, -1)
+ };
+
+ std::stringstream swc_input;
+ swc_input << "# this is a comment\n";
+ swc_input << "# this is a comment\n";
+ for (auto c : cells_orig)
+ swc_input << c << "\n";
+
+ swc_input << "# this is a final comment\n";
+ try {
+ std::size_t nr_records = 0;
+ cell_record cell;
+ while ( !(swc_input >> cell).eof()) {
+ ASSERT_LT(nr_records, cells_orig.size());
+ expect_cell_equals(cells_orig[nr_records], cell);
+ ++nr_records;
+ }
+ } catch (std::exception &e) {
+ ADD_FAILURE();
+ }
+ }
+}
+
diff --git a/main.cpp b/tests/test_tree.cpp
similarity index 58%
rename from main.cpp
rename to tests/test_tree.cpp
index ed8c3307699c64dc2ed19860d54de7739cd88e4e..3bd26796147d8d906fd88ae9b57c8708ef61e2e7 100644
--- a/main.cpp
+++ b/tests/test_tree.cpp
@@ -3,10 +3,9 @@
#include <numeric>
#include <vector>
-#include "gtest/gtest.h"
+#include "gtest.h"
#include "cell_tree.hpp"
-#include "swcio.hpp"
#include "json/src/json.hpp"
using json = nlohmann::json;
@@ -242,7 +241,7 @@ TEST(cell_tree, balance) {
// from a json file and creates a .dot file for it
TEST(cell_tree, json_load) {
json cell_data;
- std::ifstream("cells_small.json") >> cell_data;
+ std::ifstream("../data/cells_small.json") >> cell_data;
for(auto c : range(0,cell_data.size())) {
std::vector<int> parent_index = cell_data[c]["parent_index"];
@@ -252,180 +251,3 @@ TEST(cell_tree, json_load) {
}
}
-// SWC tests
-void expect_cell_equals(const neuron::io::cell_record &expected,
- const neuron::io::cell_record &actual)
-{
- EXPECT_EQ(expected.id(), actual.id());
- EXPECT_EQ(expected.type(), actual.type());
- EXPECT_FLOAT_EQ(expected.x(), actual.x());
- EXPECT_FLOAT_EQ(expected.y(), actual.y());
- EXPECT_FLOAT_EQ(expected.z(), actual.z());
- EXPECT_FLOAT_EQ(expected.radius(), actual.radius());
- EXPECT_EQ(expected.parent(), actual.parent());
-}
-
-TEST(cell_record, construction)
-{
- using namespace neuron::io;
-
- {
- // force an invalid type
- cell_record::kind invalid_type = static_cast<cell_record::kind>(100);
- EXPECT_THROW(cell_record cell(invalid_type, 7, 1., 1., 1., 1., 5),
- std::invalid_argument);
- }
-
- {
- // invalid id
- EXPECT_THROW(cell_record cell(
- cell_record::custom, -3, 1., 1., 1., 1., 5),
- std::invalid_argument);
- }
-
- {
- // invalid parent id
- EXPECT_THROW(cell_record cell(
- cell_record::custom, 0, 1., 1., 1., 1., -5),
- std::invalid_argument);
- }
-
- {
- // invalid radius
- EXPECT_THROW(cell_record cell(
- cell_record::custom, 0, 1., 1., 1., -1., -1),
- std::invalid_argument);
- }
-
- {
- // parent_id > id
- EXPECT_THROW(cell_record cell(
- cell_record::custom, 0, 1., 1., 1., 1., 2),
- std::invalid_argument);
- }
-
- {
- // parent_id == id
- EXPECT_THROW(cell_record cell(
- cell_record::custom, 0, 1., 1., 1., 1., 0),
- std::invalid_argument);
- }
-
- {
- // check standard construction by value
- cell_record cell(cell_record::custom, 0, 1., 1., 1., 1., -1);
- EXPECT_EQ(cell.id(), 0);
- EXPECT_EQ(cell.type(), cell_record::custom);
- EXPECT_EQ(cell.x(), 1.);
- EXPECT_EQ(cell.y(), 1.);
- EXPECT_EQ(cell.z(), 1.);
- EXPECT_EQ(cell.radius(), 1.);
- EXPECT_EQ(cell.diameter(), 2*1.);
- EXPECT_EQ(cell.parent(), -1);
- }
-
- {
- // check copy constructor
- cell_record cell_orig(cell_record::custom, 0, 1., 1., 1., 1., -1);
- cell_record cell(cell_orig);
- expect_cell_equals(cell_orig, cell);
- }
-}
-
-TEST(swc_parser, invalid_input)
-{
- using namespace neuron::io;
-
- {
- // check incomplete lines; missing parent
- std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830\n");
- cell_record cell;
- EXPECT_THROW(is >> cell, std::logic_error);
- }
-
- {
- // Check non-parsable values
- std::istringstream is("1a 1 14.566132 34.873772 7.857000 0.717830 -1\n");
- cell_record cell;
- EXPECT_THROW(is >> cell, std::logic_error);
- }
-
- {
- // Check invalid cell type
- std::istringstream is("1 10 14.566132 34.873772 7.857000 0.717830 -1\n");
- cell_record cell;
- EXPECT_THROW(is >> cell, std::invalid_argument);
- }
-}
-
-
-TEST(swc_parser, valid_input)
-{
- using namespace neuron::io;
-
- {
- // check empty file; no cell may be parsed
- cell_record cell, cell_orig;
- std::istringstream is("");
- EXPECT_NO_THROW(is >> cell);
- expect_cell_equals(cell_orig, cell);
- }
-
- {
- // check comment-only file not ending with a newline;
- // no cell may be parsed
- cell_record cell, cell_orig;
- std::istringstream is("#comment\n#comment");
- EXPECT_NO_THROW(is >> cell);
- expect_cell_equals(cell_orig, cell);
- }
-
-
- {
- // check last line case (no newline at the end)
- std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830 -1");
- cell_record cell;
- EXPECT_NO_THROW(is >> cell);
- EXPECT_EQ(0, cell.id()); // zero-based indexing
- EXPECT_EQ(cell_record::soma, cell.type());
- EXPECT_FLOAT_EQ(14.566132, cell.x());
- EXPECT_FLOAT_EQ(34.873772, cell.y());
- EXPECT_FLOAT_EQ( 7.857000, cell.z());
- EXPECT_FLOAT_EQ( 0.717830, cell.radius());
- EXPECT_FLOAT_EQ( -1, cell.parent());
- }
-
- {
- // check valid input with a series of records
- std::vector<cell_record> cells_orig = {
- cell_record(cell_record::soma, 0,
- 14.566132, 34.873772, 7.857000, 0.717830, -1),
- cell_record(cell_record::dendrite, 1,
- 14.566132+1, 34.873772+1, 7.857000+1, 0.717830+1, -1)
- };
-
- std::stringstream swc_input;
- swc_input << "# this is a comment\n";
- swc_input << "# this is a comment\n";
- for (auto c : cells_orig)
- swc_input << c << "\n";
-
- swc_input << "# this is a final comment\n";
- try {
- std::size_t nr_records = 0;
- cell_record cell;
- while ( !(swc_input >> cell).eof()) {
- ASSERT_LT(nr_records, cells_orig.size());
- expect_cell_equals(cells_orig[nr_records], cell);
- ++nr_records;
- }
- } catch (std::exception &e) {
- ADD_FAILURE();
- }
- }
-}
-
-int main(int argc, char **argv) {
- ::testing::InitGoogleTest(&argc, argv);
- return RUN_ALL_TESTS();
-}
diff --git a/vector b/vector
index 9c86d0a84efed0dd739888503d275378df67fe71..79ad5236b219a7618a8cda8caad6cd3de1f9e122 160000
--- a/vector
+++ b/vector
@@ -1 +1 @@
-Subproject commit 9c86d0a84efed0dd739888503d275378df67fe71
+Subproject commit 79ad5236b219a7618a8cda8caad6cd3de1f9e122