diff --git a/image_processing/build_dataset.py b/image_processing/build_dataset.py index 3cb21651966a3b3d65f1937077c0a74d18971ea2..4c7456910c6a0253a6fbf6154dadd46e378d0e80 100644 --- a/image_processing/build_dataset.py +++ b/image_processing/build_dataset.py @@ -101,14 +101,13 @@ antibiotic_enterrobacter_breakpoints = { } -def create_antibio_dataset(path='/data/label_raw/230804_strain_peptides_antibiogram_Enterobacterales.xlsx',suffix='-d200',base_path=None): +def create_antibio_dataset(path='data/label_raw/230804_strain_peptides_antibiogram_Enterobacterales.xlsx',suffix='-d200',base_path=None): """ Extract and build file name corresponding to each sample and transform antioresistance measurements to labels :param suffix: file suffix :param path: excel path :return: dataframe """ - print('base path ', base_path, 'path : ',os.path.join(base_path,path)) df = pd.read_excel(os.path.join(base_path,path), header=1) df = df[['sample_name','species','AMC (disk)','AMK (disk)','AMK (mic)','AMK (vitek)','AMP (vitek)','AMX (disk)', 'AMX (vitek)','ATM (disk)','ATM (vitek)','CAZ (disk)','CAZ (mic)','CAZ (vitek)','CHL (vitek)','CIP (disk)', @@ -180,8 +179,8 @@ def create_dataset(bin_mz=1,tolerance=0.005,noise=1000,apex='apex',suffix='-d200 name = label[label['path_aer'] == path.split("/")[-1]]['sample_name'].values[0] analyse = 'AER' if species is not None: #save image in species specific dir - directory_path_png = os.path.join(base_path,'/data/processed_data_wiff_clean_{}_{}_{}_{}/png_image/{}'.format(tolerance_str,noise,apex,bin_mz,species)) - directory_path_npy = os.path.join(base_path,'/data/processed_data_wiff_clean_{}_{}_{}_{}/npy_image/{}'.format(tolerance_str,noise,apex,bin_mz,species)) + directory_path_png = os.path.join(base_path,'data/processed_data_wiff_clean_{}_{}_{}_{}/png_image/{}'.format(tolerance_str,noise,apex,bin_mz,species)) + directory_path_npy = os.path.join(base_path,'data/processed_data_wiff_clean_{}_{}_{}_{}/npy_image/{}'.format(tolerance_str,noise,apex,bin_mz,species)) if not os.path.isdir(directory_path_png): os.makedirs(directory_path_png) if not os.path.isdir(directory_path_npy):