In [ ]:
import os
import sys
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from matplotlib import gridspec
%matplotlib notebook
In [2]:
root_folder = os.path.dirname(os.getcwd())
sys.path.append(root_folder)
import NeuNorm as neunorm
from NeuNorm.normalization import Normalization
from NeuNorm.roi import ROI
In [3]:
path_im = '../data/sample'
assert os.path.exists(path_im)
In [4]:
path_ob = '../data/ob/'
ob1 = path_ob + '0001.tif'
ob2 = path_ob + '0002.tif'
assert os.path.exists(ob1)
assert os.path.exists(ob2)
In [5]:
o_norm = Normalization()
o_norm.load(folder=path_im)
o_norm.load(file=[ob1, ob2], data_type='ob')
In [6]:
norm_roi = ROI(x0=3, y0=5, width=20, height=40)
o_norm.normalization(roi=norm_roi)
Out[6]:
True
In [7]:
normalized_data = o_norm.data['normalized']
In [8]:
np.shape(normalized_data)
Out[8]:
(15, 100, 100)
In [9]:
roi_to_keep = ROI(x0=0, y0=0, width=2, height=2)
o_norm.crop(roi=roi_to_keep)
norm_crop = o_norm.data['normalized']
np.shape(norm_crop)
Out[9]:
(15, 3, 3)
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