def gif_vp_img(self, duration, pattern='circle'):
fn = 'view_animation_' + str(self.cfg.params[self.cfg.ptc_leng]) + 'px'
vp_img_arr = Normalizer(self._vp_img_arr).uint8_norm()
dims = self._vp_img_arr.shape[:2]
r = int(min(dims) / 2)
mask = [[0] * dims[1] for _ in range(dims[0])]
if pattern == 'square':
mask[0, :] = 1
mask[:, 0] = 1
mask[-1, :] = 1
mask[:, -1] = 1
if pattern == 'circle':
for x in range(-r, r + 1):
for y in range(-r, r + 1):
if int(sqrt(x**2 + y**2)) == r:
mask[y + r][x + r] = 1
# extract coordinates from mask
coords_table = [(y, x) for y in range(len(mask))
for x in range(len(mask)) if mask[y][x]]
# sort coordinates in angular order
coords_table.sort(
key=lambda coords: atan2(coords[0] - r, coords[1] - r))
img_set = []
for coords in coords_table:
img_set.append(vp_img_arr[coords[0], coords[1], :, :, :])
misc.save_gif(img_set, duration=duration, fp=self.cfg.exp_path, fn=fn)
return True
def gif_vp_img(vp_img_arr, duration, fp='', fn='', pattern='circle'):
dims = vp_img_arr.shape[:2]
r = int(min(dims)/2)
mask = [[0] * dims[1] for _ in range(dims[0])]
if pattern == 'square':
mask[0, :] = 1
mask[:, 0] = 1
mask[-1, :] = 1
mask[:, -1] = 1
if pattern == 'circle':
for x in range(-r, r+1):
for y in range(-r, r+1):
if int(sqrt(x**2 + y**2)) == r:
mask[y+r][x+r] = 1
# extract coordinates from mask
coords_table = [(y, x) for y in range(len(mask)) for x in range(len(mask)) if mask[y][x]]
# sort coordinates in angular order
coords_table.sort(key=lambda coords: atan2(coords[0]-r, coords[1]-r))
img_set = []
for coords in coords_table:
img_set.append(vp_img_arr[coords[0], coords[1], :, :, :])
misc.save_gif(img_set, duration, fp, fn)
return True
def main(self):
# print status
self.sta.status_msg('Refocusing', self.cfg.params[self.cfg.opt_prnt])
self.sta.progress(None, self.cfg.params[self.cfg.opt_prnt])
if self.vp_img_arr is not None:
self.refo_from_vp()
elif self.lfp_img is not None:
if self.cfg.params[self.cfg.opt_refi]:
self.refo_from_scratch_upsample()
else:
self.refo_from_scratch()
# tbd
self.all_in_focus()
# check interrupt status
if not self.sta.interrupt:
# export refocused images
lfp_exporter.export_refo_stack(np.array(self._refo_stack),
self.cfg,
type='png')
# export gif animation
fn = 'refocus_animation_' + str(
self.cfg.params[self.cfg.ptc_leng]) + 'px'
misc.save_gif(misc.uint8_norm(
np.array(self._refo_stack + self._refo_stack[::-1])),
duration=.8,
fp=os.path.splitext(
self.cfg.params[self.cfg.lfp_path])[0],
fn=fn)
return True
def gif_refo(self):
# export gif animation
fn = 'refocus_animation_' + str(self.cfg.params[self.cfg.ptc_leng]) + 'px'
refo_stack = misc.Normalizer(np.asarray(self._refo_stack)).uint8_norm()
refo_stack = np.concatenate((refo_stack, refo_stack[::-1]), axis=0) # play forward and backwards
misc.save_gif(refo_stack, duration=.5, fp=self.cfg.exp_path, fn=fn)
return True
def gif_vp_img(self, duration, pattern='circle'):
lf_radius = min(int((max(self.cfg.calibs[self.cfg.ptc_mean])+1)//4), self._C)
fn = 'view_animation_' + str(lf_radius*2+1) + 'px'
img_set = self.reorder_vp_arr(pattern=pattern, lf_radius=lf_radius)
img_set = Normalizer(img_set, dtype=self.vp_img_arr.dtype).uint8_norm()
misc.save_gif(img_set, duration=duration, fp=self.cfg.exp_path, fn=fn)
return True
def gif_refo(self):
# image normalization
refo_stack = misc.Normalizer(self.refo_stack).uint8_norm()
# append reversed array copy to play forward and backwards
refo_stack = np.concatenate((refo_stack, refo_stack[::-1]), axis=0)
# export gif animation
fn = 'refocus_animation_' + str(
self.cfg.params[self.cfg.ptc_leng]) + 'px'
misc.save_gif(refo_stack, duration=.5, fp=self.cfg.exp_path, fn=fn)
return True
def gif_vp_img(self, duration, pattern='circle'):
# micro image size estimate
M = max(self.cfg.calibs[self.cfg.ptc_mean]
) if self.cfg.calibs else self.cfg.params[self.cfg.ptc_leng]
# filter images forming a pattern
lf_radius = min(int((M + 1) // 4), self._C)
img_set = self.reorder_vp_arr(pattern=pattern, lf_radius=lf_radius)
# image normalization
img_set = misc.Normalizer(img_set).uint8_norm()
# export gif animation
fn = 'view_animation_' + str(lf_radius * 2 + 1) + 'px'
misc.save_gif(img_set, duration=duration, fp=self.cfg.exp_path, fn=fn)
return True