Commit aea99cc7 authored by Alessia Marcolini's avatar Alessia Marcolini
Browse files

Link files in bbox folders

parent 9d5a91fc
......@@ -4,7 +4,7 @@ import pandas as pd
import numpy as np
from functools import reduce
from pathlib import Path
import shutil
import subprocess
from config import get_project_root
......@@ -12,7 +12,14 @@ from config import get_project_root
PROJECT_ROOT = get_project_root()
DATASETS = ['HN_val', 'HN_BZ']
BBOX_SUBDATASETS_NAMES = ['bbox_64', 'bbox_64']
BBOX_SUBDATASETS_PATHS = [
PROJECT_ROOT / 'data' / dataset / 'processed' / 'bbox' / bbox_name
for dataset, bbox_name in zip(DATASETS, BBOX_SUBDATASETS_NAMES)
]
MERGED_BBOX_SUBDATASET_NAME = 'bbox_64'
print('Copying from: ', '\t'.join([str(path) for path in BBOX_SUBDATASETS_PATHS]))
# %%
# find union names in datasets
DATASETS_NAME_UNION = list(
......@@ -22,12 +29,20 @@ DATASETS_NAME_UNION = list(
# rearrange name order (HN should be first)
DATASETS_NAME_UNION.insert(0, DATASETS_NAME_UNION.pop(DATASETS_NAME_UNION.index('HN')))
NEW_DATASET_NAME = '_'.join(DATASETS_NAME_UNION)
os.makedirs(
PROJECT_ROOT / 'data' / NEW_DATASET_NAME / 'processed' / 'bbox', exist_ok=False
NEW_DATASET_PATH = (
PROJECT_ROOT
/ 'data'
/ NEW_DATASET_NAME
/ 'processed'
/ 'bbox'
/ MERGED_BBOX_SUBDATASET_NAME
)
os.makedirs(NEW_DATASET_PATH, exist_ok=False)
print('Copying into: ', str(NEW_DATASET_PATH))
#%% [markdown]
# Merge and create a new file clinical
# # Merge and create a new clinical file
#%%
clinicals = []
dataset_name = []
......@@ -40,7 +55,9 @@ for dataset in DATASETS:
clinicals.append(clinical)
merged_clinical = pd.concat([i for i in clinicals], join='inner')
merged_clinical['dataset'] = dataset_name
merged_clinical.to_csv(
PROJECT_ROOT
/ 'data'
......@@ -49,4 +66,9 @@ merged_clinical.to_csv(
/ f'clinical_{NEW_DATASET_NAME}.csv',
index=False,
)
#%% [markdown]
# # Link files from respective folders
for old_path in BBOX_SUBDATASETS_PATHS:
subprocess.call(f'ln -s {old_path}/* {NEW_DATASET_PATH}', shell=True)
# %%
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