From 626f422749996cb66e327554a1e593ef756377d9 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 10 Sep 2024 14:55:37 +0100
Subject: [PATCH] TEST: Unit tests for splinterpolator
---
test/Makefile | 42 +++++
test/feedsRun | 14 ++
test/test_splinterpolator.cc | 170 ++++++++++++++++++
test/test_splinterpolator/data.nii.gz | 3 +
.../order_1_3d_extrap_constant_values.nii.gz | 3 +
...order_1_3d_extrap_soft_zeros_values.nii.gz | 3 +
.../order_1_3d_extrap_zeros_values.nii.gz | 3 +
...order_3_3d_extrap_constant_gradient.nii.gz | 3 +
.../order_3_3d_extrap_constant_values.nii.gz | 3 +
...der_3_3d_extrap_soft_zeros_gradient.nii.gz | 3 +
...order_3_3d_extrap_soft_zeros_values.nii.gz | 3 +
.../order_3_3d_extrap_zeros_gradient.nii.gz | 3 +
.../order_3_3d_extrap_zeros_values.nii.gz | 3 +
13 files changed, 256 insertions(+)
create mode 100644 test/Makefile
create mode 100755 test/feedsRun
create mode 100644 test/test_splinterpolator.cc
create mode 100644 test/test_splinterpolator/data.nii.gz
create mode 100644 test/test_splinterpolator/order_1_3d_extrap_constant_values.nii.gz
create mode 100644 test/test_splinterpolator/order_1_3d_extrap_soft_zeros_values.nii.gz
create mode 100644 test/test_splinterpolator/order_1_3d_extrap_zeros_values.nii.gz
create mode 100644 test/test_splinterpolator/order_3_3d_extrap_constant_gradient.nii.gz
create mode 100644 test/test_splinterpolator/order_3_3d_extrap_constant_values.nii.gz
create mode 100644 test/test_splinterpolator/order_3_3d_extrap_soft_zeros_gradient.nii.gz
create mode 100644 test/test_splinterpolator/order_3_3d_extrap_soft_zeros_values.nii.gz
create mode 100644 test/test_splinterpolator/order_3_3d_extrap_zeros_gradient.nii.gz
create mode 100644 test/test_splinterpolator/order_3_3d_extrap_zeros_values.nii.gz
diff --git a/test/Makefile b/test/Makefile
new file mode 100644
index 0000000..75e2eb5
--- /dev/null
+++ b/test/Makefile
@@ -0,0 +1,42 @@
+# A Makefile for miscmaths unit tests.
+include ${FSLCONFDIR}/default.mk
+
+PROJNAME = test-miscmaths
+TESTXFILES = test-miscmaths
+USRINCFLAGS = -DMISCMATHS_TEST_DIRECTORY=\"$(realpath .)\"
+LIBS = -lfsl-miscmaths -lfsl-NewNifti -lfsl-cprob
+
+# The test program can be run against
+# an in-source checkout, or against
+# an installed version of the
+# libfsl-miscmaths.so library.
+#
+# If the former, the miscmaths library
+# must have been compiled before the
+# test can be compiled.
+
+# The test program uses the Boost unit
+# testing framework, which needs librt
+# # on linux.
+SYSTYPE := $(shell uname -s)
+ifeq ($(SYSTYPE), Linux)
+LIBS += -lrt
+RPATH := -Wl,-rpath,'$$ORIGIN/..'
+endif
+ifeq ($(SYSTYPE), Darwin)
+RPATH := -Wl,-rpath,'@executable_path/..'
+endif
+
+all: ${TESTXFILES}
+
+OBJS := $(wildcard test_*.cc)
+OBJS := $(OBJS:%.cc=%.o)
+
+# We add -I.., -L.., -Wl,-rpath so that
+# in-source builds take precedence over
+# $FSLDEVDIR/$FSLDIR
+%.o: %.cc
+ $(CXX) -I.. ${CXXFLAGS} -c -o $@ $<
+
+test-miscmaths: ${OBJS}
+ $(CXX) ${CXXFLAGS} -o $@ $^ -L.. ${RPATH} ${LDFLAGS}
diff --git a/test/feedsRun b/test/feedsRun
new file mode 100755
index 0000000..3967fb9
--- /dev/null
+++ b/test/feedsRun
@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+
+import subprocess as sp
+import shlex
+
+def sprun(cmd):
+ print(f'RUN {cmd}')
+ sp.run(shlex.split(cmd), check=True)
+
+
+if __name__ == '__main__':
+ sprun('make clean')
+ sprun('make')
+ sprun('./test-miscmaths --report_level=detailed')
diff --git a/test/test_splinterpolator.cc b/test/test_splinterpolator.cc
new file mode 100644
index 0000000..76e9566
--- /dev/null
+++ b/test/test_splinterpolator.cc
@@ -0,0 +1,170 @@
+#define EXPOSE_TREACHEROUS
+
+#include "miscmaths/splinterpolator.h"
+#include "NewNifti/NewNifti.h"
+
+#include <armadillo>
+
+#include <filesystem>
+#include <stdlib.h>
+#include <vector>
+
+#define BOOST_TEST_MODULE test_splinterpolator
+#include <boost/test/included/unit_test.hpp>
+
+namespace fs = std::filesystem;
+namespace BTF = boost::unit_test::framework;
+namespace SPL = SPLINTERPOLATOR;
+
+class TestFixture {
+
+public:
+
+ // 5x5x5 volume data to be interpolated
+ std::vector<unsigned int> dims{5, 5, 5};
+ std::vector<float> data{
+ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
+ 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
+ 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
+ 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
+ 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,
+ 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,
+ 61, 62, 63, 64, 65, 66, 67, 68, 69, 70,
+ 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
+ 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,
+ 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,
+ 101, 102, 103, 104, 105, 106, 107, 108, 109, 110,
+ 111, 112, 113, 114, 115, 116, 117, 118, 119, 120,
+ 121, 122, 123, 124, 125
+ };
+
+ // sample points, initialised in constructor
+ size_t npts;
+ std::vector<float> xpts;
+ std::vector<float> ypts;
+ std::vector<float> zpts;
+
+ // size of up-sampled volume, initialised in constructor
+ size_t xsz;
+ size_t ysz;
+ size_t zsz;
+
+ // sampled values and gradient, initialised in constructor,
+ // populated in test cases
+ std::vector<float> values;
+ std::vector<std::vector<float>> gradient;
+
+
+ TestFixture() {
+ // the data is up-sampled by 3x
+ for (float z = -4; z < 9.01; z+=1/3.0) {
+ for (float y = -4; y < 9.01; y+=1/3.0) {
+ for (float x = -4; x < 9.01; x+=1/3.0) {
+ if (std::abs(x) < 0.01) x = 0;
+ if (std::abs(y) < 0.01) y = 0;
+ if (std::abs(z) < 0.01) z = 0;
+ xpts.push_back(x);
+ ypts.push_back(y);
+ zpts.push_back(z);
+ }}}
+ npts = xpts.size();
+ xsz = 40;
+ ysz = 40;
+ zsz = 40;
+
+ // pre-allocate space to store test outputs
+ values = std::vector<float>(npts);
+ gradient.push_back(std::vector<float>(npts));
+ gradient.push_back(std::vector<float>(npts));
+ gradient.push_back(std::vector<float>(npts));
+ };
+
+ fs::path test_data_dir() {
+ return fs::path(MISCMATHS_TEST_DIRECTORY) / "test_splinterpolator";
+ }
+
+ // load a NIfTI image from the test data directory
+ std::vector<float> load_nifti(std::string filename) {
+ char* buf;
+ float* fbuf;
+ std::vector<NiftiIO::NiftiExtension> exts;
+
+ auto hdr = NiftiIO::loadImage(test_data_dir() / filename, buf, exts);
+
+ fbuf = reinterpret_cast<float*>(buf);
+
+ std::vector<float> values(hdr.nElements());
+
+ for (auto i = 0; i < hdr.nElements(); i++) {
+ values[i] = fbuf[i];
+ }
+
+ delete [] buf;
+ return values;
+ }
+
+ // compare two float vectors
+ void compare(std::vector<float> a, std::vector<float> b, float tol=1e-5) {
+ BOOST_CHECK_EQUAL(a.size(), b.size());
+ for (auto i = 0; i < a.size(); i++) {
+ BOOST_CHECK_SMALL(a[i] - b[i], tol);
+ }
+ }
+
+ // Run the test with a Splinterpolator instance
+ void run_test(const SPL::Splinterpolator<float>& spl) {
+
+ std::string test_name = BTF::current_test_case().p_name;
+
+ std::vector<float> deriv{0, 0, 0};
+
+ for (auto i = 0; i < npts; i++) {
+ values[i] = spl(xpts[i], ypts[i], zpts[i]);
+ spl.ValAndDerivs(xpts[i], ypts[i], zpts[i], deriv);
+ gradient[0][i] = deriv[0];
+ gradient[1][i] = deriv[1];
+ gradient[2][i] = deriv[2];
+ }
+
+ compare(values, load_nifti(test_name + "_values.nii.gz"));
+
+ // derivatives are only valid for interpolation of order > 1
+ if (spl.Order() > 1) {
+ std::vector<float> gradvals;
+ gradvals.insert(gradvals.end(), gradient[0].begin(), gradient[0].end());
+ gradvals.insert(gradvals.end(), gradient[1].begin(), gradient[1].end());
+ gradvals.insert(gradvals.end(), gradient[2].begin(), gradient[2].end());
+ compare(gradvals, load_nifti(test_name + "_gradient.nii.gz"));
+ }
+ }
+};
+
+
+BOOST_FIXTURE_TEST_SUITE(test_splinterpolator, TestFixture)
+
+
+BOOST_AUTO_TEST_CASE(order_1_3d_extrap_zeros) {
+ run_test(SPL::Splinterpolator<float>(data.data(), dims, SPL::Zeros, 1));
+}
+
+BOOST_AUTO_TEST_CASE(order_1_3d_extrap_soft_zeros) {
+ run_test(SPL::Splinterpolator<float>(data.data(), dims, SPL::SoftZeros, 1));
+}
+
+BOOST_AUTO_TEST_CASE(order_1_3d_extrap_constant) {
+ run_test(SPL::Splinterpolator<float>(data.data(), dims, SPL::Constant, 1));
+}
+
+BOOST_AUTO_TEST_CASE(order_3_3d_extrap_zeros) {
+ run_test(SPL::Splinterpolator<float>(data.data(), dims, SPL::Zeros, 3));
+}
+
+BOOST_AUTO_TEST_CASE(order_3_3d_extrap_soft_zeros) {
+ run_test(SPL::Splinterpolator<float>(data.data(), dims, SPL::SoftZeros, 3));
+}
+
+BOOST_AUTO_TEST_CASE(order_3_3d_extrap_constant) {
+ run_test(SPL::Splinterpolator<float>(data.data(), dims, SPL::Constant, 3));
+}
+
+BOOST_AUTO_TEST_SUITE_END()
diff --git a/test/test_splinterpolator/data.nii.gz b/test/test_splinterpolator/data.nii.gz
new file mode 100644
index 0000000..1846c9d
--- /dev/null
+++ b/test/test_splinterpolator/data.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:51ba7314b3ad94eff389b6ffa556a381809b4ff9d8b16aad87e17e516c6b026f
+size 362
diff --git a/test/test_splinterpolator/order_1_3d_extrap_constant_values.nii.gz b/test/test_splinterpolator/order_1_3d_extrap_constant_values.nii.gz
new file mode 100644
index 0000000..de98dc5
--- /dev/null
+++ b/test/test_splinterpolator/order_1_3d_extrap_constant_values.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:335ffaaf4d9d9b1dd7bb52b8290721ee842e00983997a6b85af6df65cbdc9022
+size 4830
diff --git a/test/test_splinterpolator/order_1_3d_extrap_soft_zeros_values.nii.gz b/test/test_splinterpolator/order_1_3d_extrap_soft_zeros_values.nii.gz
new file mode 100644
index 0000000..8010489
--- /dev/null
+++ b/test/test_splinterpolator/order_1_3d_extrap_soft_zeros_values.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4b46cde43b2b530cb3c0fa2c5cca80f9b98fde362daf87330846e0c9f6b8b1db
+size 9811
diff --git a/test/test_splinterpolator/order_1_3d_extrap_zeros_values.nii.gz b/test/test_splinterpolator/order_1_3d_extrap_zeros_values.nii.gz
new file mode 100644
index 0000000..15102cb
--- /dev/null
+++ b/test/test_splinterpolator/order_1_3d_extrap_zeros_values.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:83a4f6597266e765e8505b322dce73ffb180d9687ff35d2ed35e9a50bf67d5ca
+size 2848
diff --git a/test/test_splinterpolator/order_3_3d_extrap_constant_gradient.nii.gz b/test/test_splinterpolator/order_3_3d_extrap_constant_gradient.nii.gz
new file mode 100644
index 0000000..0f415ce
--- /dev/null
+++ b/test/test_splinterpolator/order_3_3d_extrap_constant_gradient.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:df6740aafbaebb0bd22298cc4e3cdd2215f1e72c4f5420bd40a1aefb38e9e6d0
+size 285334
diff --git a/test/test_splinterpolator/order_3_3d_extrap_constant_values.nii.gz b/test/test_splinterpolator/order_3_3d_extrap_constant_values.nii.gz
new file mode 100644
index 0000000..0f571fb
--- /dev/null
+++ b/test/test_splinterpolator/order_3_3d_extrap_constant_values.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:16fe794c40b86a77a10b323d5abe1647fbe1b9ce113bf91406348f42301f0d00
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diff --git a/test/test_splinterpolator/order_3_3d_extrap_soft_zeros_gradient.nii.gz b/test/test_splinterpolator/order_3_3d_extrap_soft_zeros_gradient.nii.gz
new file mode 100644
index 0000000..5cde075
--- /dev/null
+++ b/test/test_splinterpolator/order_3_3d_extrap_soft_zeros_gradient.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 138307
diff --git a/test/test_splinterpolator/order_3_3d_extrap_soft_zeros_values.nii.gz b/test/test_splinterpolator/order_3_3d_extrap_soft_zeros_values.nii.gz
new file mode 100644
index 0000000..4847f2d
--- /dev/null
+++ b/test/test_splinterpolator/order_3_3d_extrap_soft_zeros_values.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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diff --git a/test/test_splinterpolator/order_3_3d_extrap_zeros_gradient.nii.gz b/test/test_splinterpolator/order_3_3d_extrap_zeros_gradient.nii.gz
new file mode 100644
index 0000000..57563f1
--- /dev/null
+++ b/test/test_splinterpolator/order_3_3d_extrap_zeros_gradient.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 25618
diff --git a/test/test_splinterpolator/order_3_3d_extrap_zeros_values.nii.gz b/test/test_splinterpolator/order_3_3d_extrap_zeros_values.nii.gz
new file mode 100644
index 0000000..a777875
--- /dev/null
+++ b/test/test_splinterpolator/order_3_3d_extrap_zeros_values.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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--
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