def test_normalize_boxing():
mask = gen_test.generate_test_image2(hspy=False)
image = gen_test.generate_test_image2(hspy=True)
params = PAnalysis.parameters()
params.generate(store_im=True)
particles = PAnalysis.ParticleAnalysis(image, params, mask=mask)
particles.normalize_boxing()
assert particles.list[0].image.data.shape == (68, 68)
def test_store_image():
mask = gen_test.generate_test_image(hspy=False)
image = gen_test.generate_test_image(hspy=True)
p = Particle()
p.set_mask(mask)
params = PAnalysis.parameters()
params.generate()
PAnalysis.store_image(p, image, params)
nptest.assert_allclose(p.image.data, image.data[16:184, 16:184])
def test_store_maps():
mask = gen_test.generate_test_image(hspy=False)
si = gen_test.generate_test_eds()
p = Particle()
p.set_mask(mask)
params = PAnalysis.parameters()
params.generate()
PAnalysis.store_maps(p, si, params)
au_map = si.get_lines_intensity()[0]
nptest.assert_allclose(p.maps['Au'].data, au_map.data[16:184, 16:184])
def test_time_series():
image = gen_test.generate_test_image(hspy=True)
image2 = gen_test.generate_test_image(hspy=True)
images = [image, image2]
mask = gen_test.generate_test_image(hspy=False)
mask2 = gen_test.generate_test_image(hspy=False)
masks = [mask, mask2]
params = PAnalysis.parameters()
params.generate(store_im=True)
p_list = PAnalysis.ParticleAnalysisSeries(images, params)
t = PAnalysis.timeseriesanalysis(p_list)
nptest.assert_almost_equal(t['area'][:1][0], 20069.0)
def test_particleanalysis():
image = gen_test.generate_test_image(hspy=True)
mask = gen_test.generate_test_image(hspy=False)
eds = gen_test.generate_test_eds()
si = gen_test.generate_test_si()
eels = gen_test.generate_test_si('EELS')
ac = [image, eds, si, eels]
params = PAnalysis.parameters()
params.generate(store_im=True)
params.generate_eds(eds_method='CL',
elements=['Au', 'Pd'],
factors=[1.0, 1.0],
store_maps=True)
p_list = PAnalysis.ParticleAnalysis(ac, params, mask=mask)
p = p_list.list[0]
nptest.assert_almost_equal(p.properties['area']['value'], 20069.0)
assert p.properties['area']['units'] == 'nm^2'
nptest.assert_almost_equal(p.properties['circularity']['value'],
0.9095832157785668)
nptest.assert_almost_equal(
p.properties['equivalent circular diameter']['value'],
159.8519453221949)
assert p.properties['equivalent circular diameter']['units'] == 'nm'
#assert p.zone == None
nptest.assert_allclose(p.mask, mask)
nptest.assert_allclose(p.image.data, image.data[16:184, 16:184])
au_map = eds.get_lines_intensity()[0]
nptest.assert_allclose(p.maps['Au'].data, au_map.data[16:184, 16:184])
eds_particle = eds.transpose() * mask
eds_particle = eds_particle.transpose()
eds_particle_spectrum = eds_particle.sum()
nptest.assert_allclose(p.spectrum['EDS_TEM'].data,
eds_particle_spectrum.data)
nptest.assert_allclose(p.composition['Au'], 46.94530019)
nptest.assert_allclose(p.properties['x']['value'], 100.)
nptest.assert_allclose(p.properties['y']['value'], 100.)
nptest.assert_allclose(p.properties['bbox_area']['value'], 25281.0)
nptest.assert_allclose(p.properties['bbox_length']['value'],
224.8599564173221)
assert p.properties['bbox_area']['units'] == 'nm^2'
assert p.properties['bbox_length']['units'] == 'nm'
assert p.bbox == (21, 21, 180, 180)
def test_store_spectrum():
mask = gen_test.generate_test_image(hspy=False)
si = gen_test.generate_test_eds()
p = Particle()
p.set_mask(mask)
stype = 'EDS_TEM'
p.spectrum = {}
PAnalysis.store_spectrum(p, si, stype)
si_particle = si.transpose() * mask
si_particle = si_particle.transpose()
si_particle_spectrum = si_particle.sum()
nptest.assert_allclose(p.spectrum['EDS_TEM'].data,
si_particle_spectrum.data)
def test_get_composition():
mask = gen_test.generate_test_image(hspy=False)
eds = gen_test.generate_test_eds()
p = Particle()
p.set_mask(mask)
stype = 'EDS_TEM'
p.spectrum = {}
PAnalysis.store_spectrum(p, eds, stype)
params = PAnalysis.parameters()
params.generate()
params.generate_eds(eds_method='CL',
elements=['Au', 'Pd'],
factors=[1.0, 1.0])
PAnalysis.get_composition(p, params)
nptest.assert_allclose(p.composition['Au'], 46.94530019)
def test_series():
image = gen_test.generate_test_image(hspy=True)
image2 = gen_test.generate_test_image(hspy=True)
images = [image, image2]
mask = gen_test.generate_test_image(hspy=False)
mask2 = gen_test.generate_test_image(hspy=False)
masks = [mask, mask2]
params = PAnalysis.parameters()
params.generate(store_im=True)
p_list = PAnalysis.ParticleAnalysisSeries(images, params)
p = p_list.list[0]
nptest.assert_almost_equal(p.properties['area']['value'], 20069.0)
assert p.properties['area']['units'] == 'nm^2'
nptest.assert_almost_equal(p.properties['circularity']['value'],
0.9095832157785668)
nptest.assert_allclose(p.mask, mask)
nptest.assert_allclose(p.image.data, image.data[16:184, 16:184])
nptest.assert_allclose(p.properties['x']['value'], 100.)
nptest.assert_allclose(p.properties['y']['value'], 100.)
assert p.properties['frame']['value'] == 0
def test_params_in_out():
params = PAnalysis.parameters()
params.load()
params.save()