Update Background_Substraction.py

Background_Substraction.py

@@ -51,7 +51,7 @@ warnings.filterwarnings('ignore', category= UserWarning)
 #set_name = 'Set_A'
 #set_name = 'test'
 
-'''
+
 present_dir = os.path.dirname(os.path.realpath(__file__))
 
 input_path = os.path.join(present_dir, 'wetransfer_data-zip_2024-05-17_1431')
@@ -138,68 +138,6 @@ compare_headers(exp_cols, metadata.columns.values, "Marker metadata file")
 metadata = metadata.dropna()
 metadata.head()
 
-'''
-import os
-
-# Get the current script directory
-present_dir = os.path.dirname(os.path.realpath(__file__))
-
-# Define the input path
-input_path = os.path.join(present_dir, 'wetransfer_data-zip_2024-05-17_1431')
-base_dir = input_path
-set_path = 'test'
-selected_metadata_files = ['Slide_B_DD1s1.one_1.tif.csv', 'Slide_B_DD1s1.one_2.tif.csv']
-ls_samples = ['Ashlar_Exposure_Time.csv', 'new_data.csv', 'DD3S1.csv', 'DD3S2.csv', 'DD3S3.csv', 'TMA.csv']
-
-set_name = set_path
-
-# Project and step names
-project_name = set_name               # Project name
-step_suffix = 'bs'                    # Current part (here part II)
-previous_step_suffix_long = "_qc_eda" # Previous part (here QC/EDA NOTEBOOK)
-
-# Initial input data directory
-input_data_dir = os.path.join(base_dir, project_name + previous_step_suffix_long) 
-
-# Define writable directory
-writable_directory = '/tmp'
-
-# BS output directories redirected to writable directory
-output_data_dir = os.path.join(writable_directory, project_name + "_" + step_suffix)
-# BS images subdirectory redirected to writable directory
-output_images_dir = os.path.join(output_data_dir, "images")
-
-# Metadata directories
-metadata_dir = os.path.join(base_dir, project_name + "_metadata")
-# images subdirectory
-metadata_images_dir = os.path.join(metadata_dir, "images")
-
-# Ensure the output directories exist
-os.makedirs(output_data_dir, exist_ok=True)
-os.makedirs(output_images_dir, exist_ok=True)
-
-# Print paths to verify
-print("Input Data Directory:", input_data_dir)
-print("Output Data Directory:", output_data_dir)
-print("Output Images Directory:", output_images_dir)
-print("Metadata Directory:", metadata_dir)
-print("Metadata Images Directory:", metadata_images_dir)
-
-# Example of writing a file to the new output directory
-example_data = {'Column1': [1, 2, 3], 'Column2': ['A', 'B', 'C']}
-example_df = pd.DataFrame(example_data)
-
-output_file_path = os.path.join(output_data_dir, 'example_output.csv')
-
-try:
-    example_df.to_csv(output_file_path, index=False)
-    print(f"Output written successfully to {output_file_path}")
-except PermissionError as e:
-    print(f"Permission denied: Unable to write the file at {output_file_path}. Error: {e}")
-except Exception as e:
-    print(f"An error occurred: {e}")
-
-
 # ### II.3.2. NOT_INTENSITIES
 
 # In[10]: