Extract all files + suppress warnings

02_radiomics_features_extraction/extract_features_radiomics.py

@@ -10,7 +10,9 @@ from pathlib import Path
 from tqdm import tqdm
 
 from multiproc import ListMultiprocessing
+import warnings
 
+warnings.filterwarnings("ignore")
 # %%
 DATASET = Path('HN_val')
 BBOX = 'bbox_64'
@@ -20,12 +22,10 @@ SCAN_NAMES = ['CT', 'PT']  # you are lucky that CT scans are the first in the st
 N_JOBS = 32
 N_BINS = [8, 16, 32, 64]
 PIXEL_SPACING = [1.0, 2.0, 3.0, 4.0, 5.0]
-
 #%%
 DATADIR = Path('data') / DATASET / 'processed' / 'bbox' / BBOX
 OUTDIR = Path('data') / DATASET / 'processed'
-OUTFILE = f'radiomics_features_{BBOX}_prova.csv'  # output file name
-os.chdir('..')
+OUTFILE = f'radiomics_features_{BBOX}.csv'  # output file name
 clinical = pd.read_csv(Path('data') / DATASET / 'processed' / f'clinical_{DATASET}.csv')
 
 #%%
@@ -38,7 +38,7 @@ extractor_intensity = featureextractor.RadiomicsFeaturesExtractor(params_intensi
 params_texture = 'texture.yaml'  # param file to use to create the extractor
 extractor_texture = featureextractor.RadiomicsFeaturesExtractor(params_texture)
 
-filenames = [f for f in os.listdir(DATADIR) if f.endswith('.npy')][:3]
+filenames = [f for f in os.listdir(DATADIR) if f.endswith('.npy')]
 
 exclude_list = []
 #     'HN-CHUM-011',