Commit 41d68d4e authored by Alessia Marcolini's avatar Alessia Marcolini
Browse files

Extract all files + suppress warnings

parent f66b733a
...@@ -10,7 +10,9 @@ from pathlib import Path ...@@ -10,7 +10,9 @@ from pathlib import Path
from tqdm import tqdm from tqdm import tqdm
from multiproc import ListMultiprocessing from multiproc import ListMultiprocessing
import warnings
warnings.filterwarnings("ignore")
# %% # %%
DATASET = Path('HN_val') DATASET = Path('HN_val')
BBOX = 'bbox_64' BBOX = 'bbox_64'
...@@ -20,12 +22,10 @@ SCAN_NAMES = ['CT', 'PT'] # you are lucky that CT scans are the first in the st ...@@ -20,12 +22,10 @@ SCAN_NAMES = ['CT', 'PT'] # you are lucky that CT scans are the first in the st
N_JOBS = 32 N_JOBS = 32
N_BINS = [8, 16, 32, 64] N_BINS = [8, 16, 32, 64]
PIXEL_SPACING = [1.0, 2.0, 3.0, 4.0, 5.0] PIXEL_SPACING = [1.0, 2.0, 3.0, 4.0, 5.0]
#%% #%%
DATADIR = Path('data') / DATASET / 'processed' / 'bbox' / BBOX DATADIR = Path('data') / DATASET / 'processed' / 'bbox' / BBOX
OUTDIR = Path('data') / DATASET / 'processed' OUTDIR = Path('data') / DATASET / 'processed'
OUTFILE = f'radiomics_features_{BBOX}_prova.csv' # output file name OUTFILE = f'radiomics_features_{BBOX}.csv' # output file name
os.chdir('..')
clinical = pd.read_csv(Path('data') / DATASET / 'processed' / f'clinical_{DATASET}.csv') clinical = pd.read_csv(Path('data') / DATASET / 'processed' / f'clinical_{DATASET}.csv')
#%% #%%
...@@ -38,7 +38,7 @@ extractor_intensity = featureextractor.RadiomicsFeaturesExtractor(params_intensi ...@@ -38,7 +38,7 @@ extractor_intensity = featureextractor.RadiomicsFeaturesExtractor(params_intensi
params_texture = 'texture.yaml' # param file to use to create the extractor params_texture = 'texture.yaml' # param file to use to create the extractor
extractor_texture = featureextractor.RadiomicsFeaturesExtractor(params_texture) 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 = [] exclude_list = []
# 'HN-CHUM-011', # 'HN-CHUM-011',
......
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