def test_prep_schema():
sch_f = detector_grid(shape=5, spacing=1)
sch_x = detector_grid(
shape=5,
spacing=1,
extra_dims={'illumination': ['red', 'green', 'blue']})
wl_f = 0.5
wl_l = [0.5, 0.6, 0.7]
wl_d = OrderedDict([('red', 0.5), ('green', 0.6), ('blue', 0.7)])
wl_x = xr.DataArray([0.5, 0.6, 0.7],
dims='illumination',
coords={'illumination': ['red', 'green', 'blue']})
pol_f = (0, 1)
pol_d = OrderedDict([('red', (0, 1)), ('green', (1, 0)),
('blue', (0.5, 0.5))])
pol_x = xr.concat(
[to_vector((0, 1)),
to_vector((1, 0)),
to_vector((0.5, 0.5))], wl_x.illumination)
all_in = prep_schema(sch_x, 1, wl_x, pol_x)
assert_obj_close(prep_schema(sch_x, 1, wl_d, pol_d), all_in)
assert_obj_close(prep_schema(sch_x, 1, wl_l, pol_d), all_in)
assert_obj_close(prep_schema(sch_f, 1, wl_x, pol_x), all_in)
def calc_cross_sections(scatterer, medium_index=None, illum_wavelen=None,
illum_polarization=None, theory='auto'):
"""
Calculate scattering, absorption, and extinction
cross sections, and asymmetry parameter <cos \theta>.
Parameters
----------
scatterer : :class:`.scatterer` object
(possibly composite) scatterer for which to compute scattering
medium_index : float or complex
Refractive index of the medium in which the scatter is imbedded
illum_wavelen : float or ndarray(float)
Wavelength of illumination light. If illum_wavelen is an array result
will add a dimension and have all wavelengths
theory : :class:`.theory` object (optional)
Scattering theory object to use for the calculation. This is
optional if there is a clear choice of theory for your scatterer.
If there is not a clear choice, `calc_cross_sections` will error
out and ask you to specify a theory
Returns
-------
cross_sections : array (4)
Dimensional scattering, absorption, and extinction
cross sections, and <cos theta>
"""
theory = interpret_theory(scatterer, theory)
cross_section = theory.calculate_cross_sections(
scatterer=scatterer.guess,
medium_wavevec=2*np.pi/(illum_wavelen/medium_index),
medium_index=medium_index,
illum_polarization=to_vector(illum_polarization))
return cross_section
def test_raw_fields():
sp = Sphere(r=.5, n=1.6, center=(10, 10, 5))
wavelen = .66
index = 1.33
pol = to_vector((0, 1))
sch = detector_grid(3, .1)
wavevec=2*np.pi/(wavelen/index)
pos = Mie._transform_to_desired_coordinates(
sch, (10, 10, 5), wavevec=wavevec)
rf = Mie()._raw_fields(
pos, sp, medium_wavevec=wavevec, medium_index=index,
illum_polarization=pol)
assert_allclose(rf, [[(0.0015606995428858754-0.0019143174710834162j),
(-0.0003949071974815011-0.0024154494284017187j),
(-0.002044525390662322-0.001302770747742109j),
(-0.0003949071974815009-0.002415449428401719j),
(-0.002055824337886397-0.0012853546864338861j),
(-0.00230285180386436+0.000678693819245102j),
(-0.0020445253906623225-0.0013027707477421095j),
(-0.0023028518038643603+0.0006786938192451026j),
(-0.0010011090105680883+0.0021552249454706712j)],
[(-0.0010507058414478587+0.0036584360153097306j),
(0.0020621595919700776+0.003210547679920805j),
(0.0037794246074692407+0.000585690417403587j),
(0.0020542215584045407+0.0031619947065620246j),
(0.0037426710578253295+0.000527040269055415j),
(0.002871631795307833-0.002470099566862354j),
(0.0036968090916832948+0.0005330478443315597j),
(0.002824872178181336-0.0024563186266035124j),
(2.261564613123139e-06-0.003751168280253104j)],
[(0.0010724312167657794+0.0039152445632936j),
(0.003651474601303447+0.0017688083711547462j),
(0.003740131549224567-0.001566271371618957j),
(0.0036883581831347947+0.0017866751223785315j),
(0.0037648739662344477-0.001614943488355339j),
(0.0012643679510138835-0.003894481935619062j),
(0.003816460764514863-0.0015982360934887314j),
(0.0012772696647997395-0.0039342215472070105j),
(-0.0021320123934202356-0.0035427449839031066j)]])
def load_image(inf,
spacing=None,
medium_index=None,
illum_wavelen=None,
illum_polarization=None,
normals=None,
noise_sd=None,
channel=None,
name=None):
"""
Load data or results
Parameters
----------
inf : string
File to load.
spacing : float or (float, float) (optional)
pixel size of images in each dimension - assumes square pixels if single value.
set equal to 1 if not passed in and issues warning.
medium_index : float (optional)
refractive index of the medium
illum_wavelen : float (optional)
wavelength (in vacuum) of illuminating light
illum_polarization : (float, float) (optional)
(x, y) polarization vector of the illuminating light
noise_sd : float (optional)
noise level in the image, normalized to image intensity
channel : int or tuple of ints (optional)
number(s) of channel to load for a color image (in general 0=red,
1=green, 2=blue)
name : str (optional)
name to assign the xr.DataArray object resulting from load_image
Returns
-------
obj : xarray.DataArray representation of the image with associated metadata
"""
if normals is not None:
raise ValueError(NORMALS_DEPRECATION_MESSAGE)
if name is None:
name = os.path.splitext(os.path.split(inf)[-1])[0]
with open(inf, 'rb') as pi_raw:
pi = pilimage.open(pi_raw)
arr = np.asarray(pi).astype('d')
try:
if isinstance(yaml.safe_load(pi.tag[270][0]), dict):
warnings.warn(
"Metadata detected but ignored. Use hp.load to read it.")
except (AttributeError, KeyError):
pass
extra_dims = None
if channel is None:
if arr.ndim > 2:
raise BadImage(
'Not a greyscale image. You must specify which channel(s) to use'
)
elif arr.ndim == 2:
if not channel == 'all':
warnings.warn("Not a color image (channel number ignored)")
pass
else:
# color image with specified channel(s)
if channel == 'all':
channel = range(arr.shape[2])
channel = ensure_array(channel)
if channel.max() >= arr.shape[2]:
raise LoadError(
filename, "The image doesn't have a channel number {0}".format(
channel.max()))
else:
arr = arr[:, :, channel].squeeze()
if len(channel) > 1:
# multiple channels. increase output dimensionality
if channel.max() <= 2:
channel = [['red', 'green', 'blue'][c] for c in channel]
extra_dims = {illumination: channel}
if illum_wavelen is not None and not isinstance(
illum_wavelen, dict) and len(
ensure_array(illum_wavelen)) == len(channel):
illum_wavelen = xr.DataArray(ensure_array(illum_wavelen),
dims=illumination,
coords=extra_dims)
if not isinstance(illum_polarization, dict) and np.array(
illum_polarization).ndim == 2:
pol_index = xr.DataArray(channel,
dims=illumination,
name=illumination)
illum_polarization = xr.concat(
[to_vector(pol) for pol in illum_polarization],
pol_index)
image = data_grid(arr,
spacing=spacing,
medium_index=medium_index,
illum_wavelen=illum_wavelen,
illum_polarization=illum_polarization,
noise_sd=noise_sd,
name=name,
extra_dims=extra_dims)
return image