SPROD/test_examples.py at master · longyahui/SPROD · GitHub

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# Need to install sprod first
# Need to do module purge so that the R.cpp will work
# Need R/4.0.2

import pandas as pd
import os


sprod_path = os.path.abspath(__file__)
denoise_jb = sprod_path.replace('test_examples.py', 'sprod.py')
input_path = sprod_path.replace('test_examples.py', 'test_example/input')
test_path = sprod_path.replace('test_examples.py', 'test_example/test_output')
output_path = sprod_path.replace('test_examples.py', 'test_example/expected_output')
sprod_path = sprod_path + '/sprod'

print('Removing previous testing results...', end='')
os.system('rm -rf {}/*'.format(test_path))
print('Done!')

print('Testing Sprod in single mode')
os.system(
    'python {} {} {}/single_with_img'.format(denoise_jb, input_path, test_path))
try:
    test_denoised = pd.read_csv(
        os.path.join(test_path,'single_with_img/sprod_Denoised_matrix.txt'),
        sep='\t')
    ref_denoised = pd.read_csv(
        os.path.join(output_path,'single_with_img/sprod_Denoised_matrix.txt'),
        sep='\t')
    if (test_denoised - ref_denoised).sum().sum() <= 100:
        print('Sprod test single mode succeeded!')
    else:
        print('Sprod test single mode was able to run, but the results were not expected. Please check if the input files match those in the repo.')
except FileNotFoundError:
    print('Sprod denoise job failed: no output found, please check sprod_log.txt.')

print('Testing Sprod in patches mode')
os.system(
    'python {} -y patches -pn 2 -pb 2 {} {}/batch_with_img'.format(denoise_jb, input_path, test_path))
try:
    test_denoised = pd.read_hdf(os.path.join(test_path,'batch_with_img/denoised_stiched.hdf'))
    ref_denoised = pd.read_hdf(os.path.join(output_path,'batch_with_img/denoised_stiched.hdf'))
    if (test_denoised - ref_denoised).sum().sum() <= 100:
        print('Sprod test patches mode succeeded!')
    else:
        print('Sprod test patches mode was able to run, but the results were not expected. Please check if the input files match those in the repo.')
except FileNotFoundError:
    print('Sprod denoise job failed: no output found, please check sprod_log.txt.')


print('Testing Sprod in single, pseudoimage mode')
tif_fn =os.path.join(input_path, 'image.tif')
os.rename(tif_fn, tif_fn.replace('.tif',''))
try:
    os.system(
        'python {} {} {}/single_pseudoimage'.format(denoise_jb, input_path, test_path))
    os.rename(tif_fn.replace('.tif',''), tif_fn)
except:
    os.rename(tif_fn.replace('.tif',''), tif_fn)

try:
    test_denoised = pd.read_csv(
        os.path.join(test_path,'single_pseudoimage/sprod_Denoised_matrix.txt'),
        sep='\t')
    ref_denoised = pd.read_csv(
        os.path.join(output_path,'single_pseudoimage/sprod_Denoised_matrix.txt'),
        sep='\t')
    if (test_denoised - ref_denoised).sum().sum() <= 100:
        print('Sprod test single pseudoimage mode succeeded!')
    else:
        print('Sprod test single pseudoimage mode was able to run, but the results were not expected. Please check if the input files match those in the repo.')
except FileNotFoundError:
    print('Sprod denoise job failed: no output found, please check sprod_log.txt.')

# clean up intermediate files in the input folder.
os.system('rm -rf {}/*features.csv'.format(input_path))