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Class ImagesData

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Nishchal Sapkota
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5 views2 pages

Class ImagesData

Uploaded by

Nishchal Sapkota
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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class ImagesData:

def __init__(self, df):


self.df = df

def get_vol_df(self, vol_id):


'''
input [str] : vol id (example: C57_E155_011)
output [df] : sorted dataframe by slice_index with each row
corresponding to image slice and metadata
'''
return self.df[self.df.vol_id==vol_id].sort_values(by='slice_index')

def get_vol_arr(self, vol_df):


'''
input [df] : volume df
output [numpy_array: z*h*w] : numpy array with all image slices
in the volume
'''
sample_row = vol_df.iloc[0]
z = sample_row.total_slices_count
h, w = imread(sample_row.img_path).shape
vol_arr = np.zeros((z,h,w))
index = 0
for _, row in vol_df.iterrows():
image = imread(row.img_path)
if image.max() != 0:
image = image/image.max()
vol_arr[index] = image
index += 1
return vol_arr

def process_vol_id(self, vol_id):


start = time.time()
vol_df = self.get_vol_df(vol_id)
vol_arr = self.get_vol_arr(vol_df)
print(f'{vol_id}: {time.time()-start} s.')
return vol_id, vol_arr

def get_vol_arr_dict(self):
vols_dict = {}
vols = self.df.vol_id.unique()
# for vol_id in vols:
# start = time.time()
# vols_dict[vol_id] = self.get_vol_arr(self.get_vol_df(vol_id))
# print(f'{time.time()-start} s.')
with mp.Pool(mp.cpu_count()) as pool:
results = pool.map(self.process_vol_id, vols)

start = time.time()
for vol_id, vol_arr in results:
vols_dict[vol_id] = vol_arr
print(f'{time.time()-start} s.')

return vols_dict

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