modify for python 3.9 compatibility

affine_transfo.py

@@ -120,7 +120,11 @@ def random_values(df, subject_name, config_param):
         'shift_PA': shift_PA,
         'shift_IS': shift_IS
     }
-    df = df.append(transfo_dict, ignore_index=True)
+    #df = df.append(transfo_dict, ignore_index=True)
+    print(df)
+    print(transfo_dict)
+    df_new_row = pd.DataFrame(transfo_dict, index=[0])
+    df = pd.concat([df, df_new_row], ignore_index=True)#.reset_index()
     return df, angle_IS, angle_PA, angle_LR, shift_LR, shift_PA, shift_IS
 
 

config_sct_run_batch.yml

@@ -1,10 +1,9 @@
 # config file for sct_run_batch
 path_data: ~/datasets/data-multi-subject
-path_output: ~/process_results/results_csa-atrophy_t2-all-2024-08-08
+path_output: ~/process_results/results_csa-atrophy_t2-all-2024-08-13
 script: ~/code/csa-atrophy/process_data.sh
 script_args: /home/GRAMES.POLYMTL.CA/sebeda/code/csa-atrophy/config_script.yml
-jobs: 4
+jobs: 8
 batch_log: sct_run_batch_log.txt
 continue_on_error: 1
 subject_prefix: sub-
-email_to: [email protected]

requirements.txt

@@ -6,8 +6,8 @@ scikit-image
 nibabel
 ruamel.yaml
 yaml-1.3
-argparse~=1.4.0
-setuptools~=49.6.0
-PyYAML~=5.3.1
-coloredlogs~=14.0
+argparse
+setuptools
+PyYAML
+coloredlogs
 

setup.py

@@ -29,6 +29,7 @@
     ],
     keywords='',
     install_requires=install_reqs,
+    packages = [],
     entry_points={
         'console_scripts': [
             'affine_transfo=affine_transfo:main',