1a_check_crop.py

import os
import pandas as pd
import numpy as np
from funs_support import find_dir_cell

dir_base = find_dir_cell()
dir_images = os.path.join(dir_base, 'images')
dir_output = os.path.join(dir_base, 'output')
dir_ordinal = os.path.join(dir_base,'..','GIOrdinal','data')
dir_cropped = os.path.join(dir_ordinal, 'cropped')

path_breaker = os.path.join(dir_ordinal,'df_codebreaker.csv')
df_breaker = pd.read_csv(path_breaker).drop(columns='file')
df_breaker['tissue2'] = df_breaker.file2.str.replace('.png','',regex=False).str.split('_').apply(lambda x: x[-1])
u_QID = df_breaker.QID.unique()

# Image data on the GICell side
fn_images = pd.Series(os.listdir(dir_images))
fn_images = fn_images[fn_images.str.contains('png$',regex=True)].reset_index(None,drop=True)
df_images = fn_images.str.split('\\_',2,True).drop(columns=[0])
df_images.rename(columns={1:'idt',2:'tissue'}, inplace=True)
df_images['tissue'] = df_images.tissue.str.replace('.png','',regex=False)
tmp = df_images.tissue.str.split('\\_|\\-',2,True)
tmp.rename(columns={0:'tissue',1:'num',2:'alt'}, inplace=True)
df_images = pd.concat(objs=[df_images.drop(columns='tissue'),tmp],axis=1)
df_images['fn'] = fn_images.copy()
cn_sort = ['idt','tissue','num']
df_images = df_images.sort_values(cn_sort)
u_idt = df_images.idt.unique()
# Keep only HSK images
assert len(np.setdiff1d(u_QID,u_idt))==0, 'Breaker has patients not found in folder'
df_images = df_images[df_images['idt'].isin(u_QID)].reset_index(None,drop=True)

print('Expect cleaned_6EAWUIY4_Cecum_55.png not to align because it has cecum + cecum-001')
holder_check = []
for ii, rr in df_images.iterrows():
    idt, tissue, fn = rr['idt'], rr['tissue'], rr['fn']
    path_GICell = os.path.join(dir_images, fn)
    match = df_breaker.query('QID==@idt & tissue==@tissue')
    tt = list(match['type'])[0]
    path_Ordinal, check = '', False
    for tish in match.tissue2.unique():
        path_tissue = os.path.join(dir_cropped, tt, idt, tish)
        if os.path.exists(path_tissue):
            # Remove -v2
            fn2 = pd.Series(fn).str.replace('[\\-|\\_]v2','',regex=True)
            fn2 = fn2.str.replace(tissue,tish,regex=True)[0]    
            path_Ordinal = os.path.join(path_tissue, fn2)
            if os.path.exists(path_Ordinal):
                # Check that files are the same
                check = open(path_GICell,"rb").read() == open(path_Ordinal,"rb").read()
                if not check:
                    print('file %s does not align (%i of %i)' % (fn, ii+1, len(df_images)))                    
    holder_check.append(pd.Series([path_GICell, path_Ordinal, check]))
res_check = pd.DataFrame(pd.concat(objs=holder_check,axis=1).T)
res_check.columns = ['path_Cell','path_Ordinal','check']
res_check.check = res_check.check.astype(bool)
res_check = pd.concat(objs=[df_images[cn_sort],res_check],axis=1)
print('Does not align == ')
print(res_check.loc[~res_check.check,cn_sort].T)