From 045de4aa3009b3631d45fab910349eca3fe89ef2 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Mon, 10 Apr 2017 18:20:11 +0100
Subject: [PATCH] Mesh and imagewrapper.naninfrange unit tests
---
tests/test_imagewrapper.py | 41 +
tests/test_mesh.py | 133 ++
tests/testdata/test_mesh.vtk | 1928 +++++++++++++++++++++++++++++
tests/testdata/test_mesh_data.txt | 642 ++++++++++
4 files changed, 2744 insertions(+)
create mode 100644 tests/test_mesh.py
create mode 100755 tests/testdata/test_mesh.vtk
create mode 100644 tests/testdata/test_mesh_data.txt
diff --git a/tests/test_imagewrapper.py b/tests/test_imagewrapper.py
index 8e1151929..f733ff4a2 100644
--- a/tests/test_imagewrapper.py
+++ b/tests/test_imagewrapper.py
@@ -286,6 +286,47 @@ def test_sliceTupleToSliceObj():
assert func(slices) == sliceobj
+def test_naninfrange():
+ # numinf, numnan, expectedResult
+ tests = [( 0, 0, (0, 100)),
+ ( 0, 1, (0, 100)),
+ ( 1, 0, (0, 100)),
+ ( 1, 1, (0, 100)),
+ ( 5, 5, (0, 100)),
+ ( 0, 'all', (np.nan, np.nan)),
+ ('all', 0, (np.nan, np.nan))]
+
+ # Test non floating point data as wll
+ data = np.linspace(0, 100, 100, dtype=np.uint32)
+ assert imagewrap.naninfrange(data) == (0, 100)
+
+ for numinf, numnan, expected in tests:
+
+ data = np.linspace(0, 100, 100)
+
+ if numinf == 'all': data[:] = np.inf
+ elif numnan == 'all': data[:] = np.nan
+
+ nanoff = 1
+ if numinf != 'all':
+ for i in range(1, numinf + 1):
+ data[i] = np.inf
+ nanoff += numinf
+
+ if numnan != 'all':
+ for i in range(nanoff, numnan + nanoff):
+ data[i] = np.nan
+
+ result = imagewrap.naninfrange(data)
+
+ if np.isfinite(expected[0]): assert result[0] == expected[0]
+ elif np.isnan( expected[0]): assert np.isnan(result[0])
+ elif np.isinf( expected[0]): assert np.isinf(result[0])
+ if np.isfinite(expected[1]): assert result[1] == expected[1]
+ elif np.isnan( expected[1]): assert np.isnan(result[1])
+ elif np.isinf( expected[1]): assert np.isinf(result[1])
+
+
def test_adjustCoverage():
# TODO Randomise
diff --git a/tests/test_mesh.py b/tests/test_mesh.py
new file mode 100644
index 000000000..c2d234fb1
--- /dev/null
+++ b/tests/test_mesh.py
@@ -0,0 +1,133 @@
+#!/usr/bin/env python
+#
+# test_mesh.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import os.path as op
+import shutil
+import tempfile
+
+import numpy as np
+import pytest
+
+import fsl.data.mesh as fslmesh
+
+
+datadir = op.join(op.dirname(__file__), 'testdata')
+
+
+def test_create_mesh():
+
+ # Test:
+ # - create from file
+ # - create from inmem data
+ testbase = 'test_mesh.vtk'
+ testfile = op.join(datadir, testbase)
+
+ verts, lens, indices = fslmesh.loadVTKPolydataFile(testfile)
+
+ mesh1 = fslmesh.TriangleMesh(testfile)
+ mesh2 = fslmesh.TriangleMesh(verts, indices)
+
+ assert mesh1.name == testbase
+ assert mesh2.name == 'TriangleMesh'
+ assert mesh1.dataSource == testfile
+ assert mesh2.dataSource is None
+
+ assert mesh1.vertices.shape == (642, 3)
+ assert mesh2.vertices.shape == (642, 3)
+ assert mesh1.indices.shape == (1280, 3)
+ assert mesh2.indices.shape == (1280, 3)
+
+ minbounds = np.array([ 59.50759888, 88.43039703, 72.10890198])
+ maxbounds = np.array([ 77.72619629, 128.40600586, 94.82050323])
+
+ mesh1Bounds = mesh1.getBounds()
+ mesh2Bounds = mesh2.getBounds()
+
+ assert np.all(np.isclose(mesh1Bounds[0], minbounds))
+ assert np.all(np.isclose(mesh1Bounds[1], maxbounds))
+ assert np.all(np.isclose(mesh2Bounds[0], minbounds))
+ assert np.all(np.isclose(mesh2Bounds[1], maxbounds))
+
+
+def test_mesh_loadVertexData():
+
+ meshfile = op.join(datadir, 'test_mesh.vtk')
+ datafile = op.join(datadir, 'test_mesh_data.txt')
+ memdata = np.random.randint(1, 100, 642)
+ mesh = fslmesh.TriangleMesh(meshfile)
+
+ assert mesh.loadVertexData(datafile).shape == (642,)
+ assert np.all(mesh.loadVertexData('inmemdata', memdata) == memdata)
+
+ assert mesh.getVertexData(datafile).shape == (642,)
+ assert np.all(mesh.getVertexData('inmemdata') == memdata)
+
+ mesh.clearVertexData()
+
+ assert mesh.getVertexData(datafile).shape == (642,)
+ assert np.all(mesh.loadVertexData('inmemdata', memdata) == memdata)
+
+
+def test_loadVTKPolydataFile():
+
+ testfile = op.join(datadir, 'test_mesh.vtk')
+ verts, lens, indices = fslmesh.loadVTKPolydataFile(testfile)
+
+ assert verts.shape == (642, 3)
+ assert indices.shape == (3840, )
+ assert lens.shape == (1280, )
+ assert np.all(lens == 3)
+
+
+def test_getFIRSTPrefix():
+
+ failures = [
+ 'blob.txt',
+ 'blob.vtk',
+ 'blob.nii.gz']
+
+ passes = [
+ ('blurgh-L_Thal_first.vtk', 'blurgh'),
+ ('blurgh-L_Accu_first.vtk', 'blurgh'),
+ ('blurgh_bufuu-R_Hipp_first.vtk', 'blurgh_bufuu'),
+ ]
+
+ for f in failures:
+ with pytest.raises(ValueError):
+ fslmesh.getFIRSTPrefix(f)
+
+ for fname, expected in passes:
+ assert fslmesh.getFIRSTPrefix(fname) == expected
+
+
+
+def test_findReferenceImage():
+
+ testdir = tempfile.mkdtemp()
+ vtkfiles = ['struc-L_Thal_first.vtk',
+ 'struc_first-L_Thal_first.vtk']
+
+ assert fslmesh.findReferenceImage('nofile') is None
+
+ try:
+
+ for fname in vtkfiles:
+
+ assert fslmesh.findReferenceImage(fname) is None
+
+ prefix = fslmesh.getFIRSTPrefix(fname)
+ imgfname = op.join(testdir, '{}.nii.gz'.format(prefix))
+ fname = op.join(testdir, fname)
+
+ with open(fname, 'wt') as f: f.write(fname)
+ with open(imgfname, 'wt') as f: f.write(imgfname)
+
+ assert fslmesh.findReferenceImage(fname) == imgfname
+
+ finally:
+ shutil.rmtree(testdir)
diff --git a/tests/testdata/test_mesh.vtk b/tests/testdata/test_mesh.vtk
new file mode 100755
index 000000000..72ff53830
--- /dev/null
+++ b/tests/testdata/test_mesh.vtk
@@ -0,0 +1,1928 @@
+# vtk DataFile Version 3.0
+this file was written using fslvtkio
+ASCII
+DATASET POLYDATA
+POINTS 642 float
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diff --git a/tests/testdata/test_mesh_data.txt b/tests/testdata/test_mesh_data.txt
new file mode 100644
index 000000000..96b7f4331
--- /dev/null
+++ b/tests/testdata/test_mesh_data.txt
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--
GitLab