From f91aeb22a3fe002ec2740c76b7964809f3c87084 Mon Sep 17 00:00:00 2001
From: Schneider Leo <leo.schneider@etu.ec-lyon.fr>
Date: Wed, 11 Jun 2025 16:59:43 +0200
Subject: [PATCH] fix : absolute path for image dataset and DLLs
---
image_processing/build_dataset.py | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/image_processing/build_dataset.py b/image_processing/build_dataset.py
index 3cb2165..4c74569 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):
--
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