In [1]:
import os
import sys
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from matplotlib import gridspec
%matplotlib notebook
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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
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path_ob = '../data/ob/'
assert os.path.exists(path_ob)
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path_im = '../data/sample'
assert os.path.exists(path_im)
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path_df = '../data/df'
assert os.path.exists(path_df)
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o_norm = Normalization()
o_norm.load(folder=path_im)
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o_norm.load(folder=path_ob, data_type='ob', notebook=True)
o_norm.load(folder=path_df, data_type='df')
Data type cannot be displayed:
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o_norm.df_correction()
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norm_roi = ROI(x0=3, y0=5, width=20, height=40)
o_norm.normalization(roi=norm_roi, notebook=True)
Data type cannot be displayed:
Out[9]:
True
In [20]:
normalized_data = o_norm.data['normalized']
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np.shape(normalized_data)
Out[21]:
(15, 100, 100)
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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)
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