plt.style.use('dark_background')
plt.rcParams['figure.facecolor'] = '#272b30'
plt.rcParams['image.cmap'] = 'inferno'
FORMAT = "%(asctime)s| %(levelname)s [%(filename)s: - %(funcName)20s] %(message)s"
logging.basicConfig(level=logging.INFO,
format=FORMAT)
data_path = os.path.join(sys.path[0], 'fluo_data')
all_cells = op.WDPars(data_path)
one_cell = 2
# # Fluo-4 bleachin experiment
# df = pd.DataFrame(columns=['cell', 'exp', 'cycl', 'time', 'int'])
# for cell_num in range(0, len(all_cells)):
# cell = all_cells[cell_num]
# series_int = cell.relInt()
# for single_num in range(len(series_int)):
# single_int = series_int[single_num]
# df = df.append(pd.Series([int(cell_num+1), cell.exposure, cell.cycles, int(single_num+1), single_int],
# index=df.columns),
# ignore_index=True)
# PA in loading solution experiment (1 - no PA, 2 - with PA)
# options
max_frame_number = 20 # frames after stimulation
cell_name_suffix = '_26_11' # suffix with registration date
frame_reg_time = 1.0 # frame registration time in seconds
save_csv = False
# hystTool global settings set up
h.settings(sigma=1, kernel_size=3, sd_lvl=5, high=0.8, low_init=0.005, mask_diff=50)
# registration type FluoData global settings set up
FluoData.settings(max_frame_num=max_frame_number, th_method='hyst',
dot_on=True, dot_mode='mean', dot_sigma=1, dot_kernel_size=20, dot_return_extra=True)
# records paring
all_cells = op.WDPars(data_path, name_suffix=cell_name_suffix)
df = pd.DataFrame(columns=['cell', 'power', 'stimul', 'frame', 'time', 'mask', 'int', 'delta', 'rel'])
for cell_num in range(0, len(all_cells)):
cell = all_cells[cell_num]
logging.info('Image {} in progress'.format(cell.img_name))
cell_path = f'{res_path}/{cell.img_name}'
if not os.path.exists(cell_path):
os.makedirs(cell_path)
# alex mask images
alex_up, alex_down, base_win, max_win = edge.alex_delta(cell.img_series,
mask=cell.max_frame_mask,
win_index=[12, cell.max_frame_num+1, 5],
spacer=5,
FORMAT = "%(asctime)s| %(levelname)s [%(filename)s: - %(funcName)20s] %(message)s"
logging.basicConfig(level=logging.INFO, format=FORMAT)
data_path = os.path.join(sys.path[0], 'data')
res_path = os.path.join(sys.path[0], 'memb_res')
if not os.path.exists(res_path):
os.makedirs(res_path)
all_cells = op.WDPars(
wd_path=data_path,
mode='z',
middle_frame=6, # MembData parameters
sigma=3,
kernel_size=21,
sd_area=40,
sd_lvl=2,
mean=[140, 130],
high=0.8,
low_init=0.01,
mask_diff=350) # hystTools parameters
df = pd.DataFrame(columns=['file', 'cell', 'feature', 'time', 'int'])
for cell_num in range(0, len(all_cells)):
cell = all_cells[cell_num]
logging.info('Image {} in progress'.format(cell.img_name))
cell.get_sd_surf(start_frame=1, fin_frame=14)
# plt.figure()
# ax0 = plt.subplot()