def test_non_tiff():
# test loading a few other image formats. We have some in the docs
# director, so just use them
import holopy
root = os.path.split(os.path.split(holopy.__file__)[0])[0]
doc_images = os.path.join(root, 'docs', 'source', 'images')
load(os.path.join(doc_images, 'image_5Particle_Hologram.jpg'))
load(os.path.join(doc_images, 'ReconVolume_mlab_5Particle_Hologram.png'))
def test_non_tiff():
# test loading a few other image formats. We have some in the docs
# director, so just use them
import holopy
root = os.path.split(os.path.split(holopy.__file__)[0])[0]
doc_images = os.path.join(root, 'docs', 'source', 'images')
load(os.path.join(doc_images, 'image_5Particle_Hologram.jpg'))
load(os.path.join(doc_images, 'ReconVolume_mlab_5Particle_Hologram.png'))
def test_serialization():
par_s = Sphere(center=(Uniform(0, 1e-5, guess=.567e-5),
Uniform(0, 1e-5, .567e-5), Uniform(1e-5, 2e-5)),
r=Uniform(1e-8, 1e-5, 8.5e-7),
n=Uniform(1, 2, 1.59))
alpha = Uniform(.1, 1, .6, 'alpha')
schema = update_metadata(detector_grid(shape=100, spacing=.1151e-6),
illum_wavelen=.66e-6,
medium_index=1.33,
illum_polarization=(1, 0))
model = AlphaModel(par_s,
medium_index=schema.medium_index,
illum_wavelen=schema.illum_wavelen,
alpha=alpha)
holo = calc_holo(schema, model.scatterer.guess, scaling=model.alpha.guess)
result = fix_flat(NmpfitStrategy().fit(model, holo))
temp = tempfile.NamedTemporaryFile(suffix='.h5', delete=False)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
save(temp.name, result)
loaded = load(temp.name)
assert_obj_close(result, loaded, context='serialized_result')
def test_serialization():
par_s = Sphere(center=(par(.567e-5, [0, 1e-5]), par(.576e-6, [0, 1e-5]),
par(15e-6, [1e-5, 2e-5])),
r=par(8.5e-7, [1e-8, 1e-5]),
n=par(1.59, [1, 2]))
alpha = par(.6, [.1, 1], 'alpha')
schema = ImageSchema(shape=100,
spacing=.1151e-6,
optics=Optics(.66e-6, 1.33))
model = Model(par_s, Mie.calc_holo, alpha=alpha)
holo = Mie.calc_holo(model.scatterer.guess, schema, model.alpha.guess)
result = fit(model, holo)
temp = tempfile.NamedTemporaryFile()
save(temp, result)
temp.flush()
temp.seek(0)
loaded = load(temp)
assert_obj_close(result, loaded, context='serialized_result')
def test_image_io():
holo = get_example_data('image0001.yaml')
t = tempfile.mkdtemp()
filename = os.path.join(t, 'image0001.tif')
save(filename, holo)
l = load(filename)
assert_obj_close(l, holo)
# check that it defaults to saving as tif
filename = os.path.join(t, 'image0002')
save_image(filename, holo)
l = load(filename + '.tif')
assert_obj_close(l, holo)
# check saving 16 bit
filename = os.path.join(t, 'image0003')
save_image(filename, holo, scaling=None, depth=16)
l = load(filename + '.tif')
assert_obj_close(l, holo)
# test that yaml save works corretly with a string instead of a file
filename = os.path.join(t, 'image0001.yaml')
save(filename, holo)
loaded = load(filename)
assert_obj_close(loaded, holo)
f = get_example_data_path('image0001.yaml')
spacing = .1
optics = Optics(.66, 1.33, (1, 0))
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
h = load(f, spacing=spacing, optics=optics)
assert_obj_close(h.optics, optics)
assert_equal(h.spacing, spacing)
assert_equal(len(w), 1)
assert "Overriding spacing and optics of loaded yaml" in w[-1].message
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
h = load(f, optics=optics)
assert_obj_close(h.optics, optics)
assert_equal(h.spacing, holo.spacing)
assert_equal(len(w), 1)
assert ("WARNING: overriding optics of loaded yaml without "
"overriding spacing, this is probably incorrect."
in w[-1].message)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
h = load(f, spacing=spacing)
assert_obj_close(h.optics, holo.optics)
assert_equal(h.spacing, spacing)
assert_equal(len(w), 1)
assert ("WARNING: overriding spacing of loaded yaml without "
"overriding optics, this is probably incorrect."
in w[-1].message)
shutil.rmtree(t)
def test_save_images(self):
filenames = [
os.path.join(self.tempdir, f)
for f in ['dummy_filename_1.tif', 'dummy_filename_2.tif']
]
save_images(filenames, self.holograms, scaling=None)
for ground_truth, filename in zip(self.holograms, filenames):
loaded = load(filename)
self.assertTrue(np.all(loaded.values == ground_truth.values))
def test_load_optics():
optics_yaml = """wavelen: 785e-9
polarization: [1.0, 0]
divergence: 0
pixel_size: [6.8e-6, 6.8e-6]
pixel_scale: [3.3e-7, 3.3e-7]"""
t = tempfile.TemporaryFile()
t.write(optics_yaml)
t.seek(0)
o = Optics(**load(t))
assert_obj_close(o, Optics(wavelen=7.85e-07, polarization=[1.0, 0.0], divergence=0, pixel_size=[6.8e-06, 6.8e-06], pixel_scale=[3.3e-07, 3.3e-07]))
def test_image_io():
holo = get_example_data('image0001.yaml')
t = tempfile.mkdtemp()
filename = os.path.join(t, 'image0001.tif')
save(filename, holo)
l = load(filename)
assert_obj_close(l, holo)
# check that it defaults to saving as tif
filename = os.path.join(t, 'image0002')
save_image(filename, holo)
l = load(filename+'.tif')
assert_obj_close(l, holo)
# test that yaml save works corretly with a string instead of a file
filename = os.path.join(t, 'image0001.yaml')
save(filename, holo)
loaded = load(filename)
assert_obj_close(loaded, holo)
f = get_example_data_path('image0001.yaml')
spacing = .1
optics = Optics(.66, 1.33, (1,0))
with warnings.catch_warnings(record =True) as w:
warnings.simplefilter('always')
h = load(f, spacing = spacing, optics = optics)
assert_obj_close(h.optics, optics)
assert_equal(h.spacing, spacing)
assert_equal(len(w), 1)
assert "Overriding spacing and optics of loaded yaml" in w[-1].message
with warnings.catch_warnings(record =True) as w:
warnings.simplefilter('always')
h = load(f, optics = optics)
assert_obj_close(h.optics, optics)
assert_equal(h.spacing, holo.spacing)
assert_equal(len(w), 1)
assert ("WARNING: overriding optics of loaded yaml without "
"overriding spacing, this is probably incorrect." in
w[-1].message)
with warnings.catch_warnings(record =True) as w:
warnings.simplefilter('always')
h = load(f, spacing = spacing)
assert_obj_close(h.optics, holo.optics)
assert_equal(h.spacing, spacing)
assert_equal(len(w), 1)
assert ("WARNING: overriding spacing of loaded yaml without "
"overriding optics, this is probably incorrect." in
w[-1].message)
shutil.rmtree(t)
def test_load_optics():
optics_yaml = """wavelen: 785e-9
polarization: [1.0, 0]
divergence: 0
pixel_size: [6.8e-6, 6.8e-6]
pixel_scale: [3.3e-7, 3.3e-7]"""
t = tempfile.TemporaryFile()
t.write(optics_yaml)
t.seek(0)
o = Optics(**load(t))
assert_obj_close(
o,
Optics(wavelen=7.85e-07,
polarization=[1.0, 0.0],
divergence=0,
pixel_size=[6.8e-06, 6.8e-06],
pixel_scale=[3.3e-07, 3.3e-07]))
def test_serialization():
par_s = Sphere(center = (par(.567e-5, [0, 1e-5]), par(.576e-6, [0, 1e-5]),
par(15e-6, [1e-5,
2e-5])),
r = par(8.5e-7, [1e-8, 1e-5]), n = par(1.59, [1,2]))
alpha = par(.6, [.1, 1], 'alpha')
schema = ImageSchema(shape = 100, spacing = .1151e-6, optics = Optics(.66e-6, 1.33))
model = Model(par_s, Mie.calc_holo, alpha=alpha)
holo = Mie.calc_holo(model.scatterer.guess, schema, model.alpha.guess)
result = fit(model, holo)
temp = tempfile.NamedTemporaryFile()
save(temp, result)
temp.flush()
temp.seek(0)
loaded = load(temp)
assert_obj_close(result, loaded, context = 'serialized_result')
def test_load_func_from_save_image_func_with_scaling(self):
filename = os.path.join(self.tempdir, 'image0006')
save_image(filename, self.holo, scaling='auto')
loaded = load(filename + '.tif')
assert_obj_close(np.around(loaded), self.holo)
def test_load_func_from_save_image_func(self):
filename = os.path.join(self.tempdir, 'image0006')
save_image(filename, self.holo, scaling=None)
loaded = load(filename + '.tif')
assert_obj_close(loaded, self.holo)
def test_save_load_h5(self):
filename = os.path.join(self.tempdir, 'image0001')
save(filename, self.holo)
loaded = load(filename)
assert_obj_close(loaded, self.holo)
from __future__ import print_function
import numpy as np
import holopy as hp
from holopy.propagation import propagate
from holopy.core import load
import matplotlib.pyplot as plt
import time
optics = hp.core.Optics(wavelen=0.405, index=1.33, polarization=[1.0, 0.0])
holo = load("jerichoObject.bmp", spacing=6e-6, optics=optics)
bg = load("jerichoRef.bmp", spacing=6e-6, optics=optics)
holo = holo - bg
rec_vol = propagate(holo, np.linspace(245e-6, 250e-6, 5))
plt.ion()
fig = plt.figure()
ax = fig.gca()
for i in xrange(rec_vol.shape[2]):
print(i)
# name='figure%d.png'%(i,)
# plt.savefig(name,bbox_inches=0)
plt.clf()
plt.imshow(rec_vol[..., i].real, cmap=plt.cm.Greys_r)
fig.canvas.draw()
time.sleep(1)
