Mesh and imagewrapper.naninfrange unit tests

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

tests/test_mesh.py

+#!/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)

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