def test_subimage():
i = detector_grid(shape=(10, 10), spacing=1)
s = subimage(i, (5, 5), 2)
assert s.shape == (1, 2, 2)
i2 = data_grid(i, 1)
s2 = subimage(i2, (5, 5), 2)
def test_subimaged():
# make a dummy image so that we can pretend we are working with
# data we want to subimage
im = xschema
h = calc_holo(im, sphere, index, wavelen, xpolarization)
sub = (60, 70), 30
hs = calc_holo(subimage(im, *sub), sphere, index, wavelen, xpolarization)
assert_obj_close(subimage(h, *sub), hs)
def load_bgdivide_crop_v2(
path, metadata, particle_position, bkg, dark, channel=RGB_CHANNEL,
size=HOLOGRAM_SIZE):
data = hp.load_image(path, channel=channel, **metadata)
data = bg_correct(data, bkg, dark)
data = subimage(data, particle_position[::-1], size)
data = normalize(data)
return data
def load_bgdivide_crop(
path, metadata, particle_position, bg_prefix="bg", df_prefix=None,
channel=RGB_CHANNEL, size=HOLOGRAM_SIZE):
data = hp.load_image(path, channel=channel, **metadata)
bkg = load_bkg(path, bg_prefix, refimg=data)
dark = None # load_dark(path, df_prefix, refimg=data)
data = bg_correct(data, bkg, dark)
data = subimage(data, particle_position[::-1], size)
data = normalize(data)
return data
def load_bgdivide_crop(path,
metadata,
particle_position,
bkg,
dark,
channel=RGB_CHANNEL,
size=HOLOGRAM_SIZE,
recenter=True):
data = hp.load_image(path, channel=channel, **metadata)
data = bg_correct(data, bkg, dark)
if recenter:
bbox = subimage(data, particle_position, size)
bbox_corner = np.array([bbox.x.min(), bbox.y.min()])
found_position = np.round(
center_find(bbox) + bbox_corner / metadata['spacing'])
data = subimage(data, found_position, size)
else:
data = subimage(data, particle_position, size)
data = normalize(data)
if recenter:
return data, found_position
return data, None
def test_ps():
imagepath = get_example_data_path('ps_image01.jpg')
bgpath = get_example_data_path('ps_bg01.jpg')
L = 0.0407 # distance from light source to screen
cam_spacing = 12e-6 # linear size of camera pixels
mag = 9.0 # magnification
npix_out = 1020 # linear size of output image (pixels)
zstack = [1.08e-3, 1.18e-3] # distances from camera to reconstruct
holo = load_image(imagepath, spacing=cam_spacing, illum_wavelen=406e-9, medium_index=1) # load hologram
bg = load_image(bgpath, spacing=cam_spacing) # load background image
holo = bg_correct(holo, bg+1, bg) # subtract background
holo = subimage(holo,[250,500],300)
beam_c = center_of_mass(bg.values.squeeze()) # get beam center
simplefilter('ignore')
recons = ps_propagate(holo, zstack, L, beam_c) # do propagation
verify(recons, 'ps_recon')
def test_subimage_floats():
i = data_grid(np.zeros((100, 100)), .1)
s1 = subimage(i, (5.2, 5.6), 2)
s2 = subimage(i, (5, 6), 2)
assert_obj_close(s1, s2)
def _load_data(self, name): # need metadata, particle_position!
data = hp.load_image(name, channel=RGB_CHANNEL, **self.metadata)
data = bg_correct(data, self._background, self._darkfield)
data = subimage(data, self.particle_position[::-1], HOLOGRAM_SIZE)
data = normalize(data)
return data