Update Background_Substraction.py

Background_Substraction.py

@@ -50,6 +50,8 @@ 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')
@@ -104,7 +106,6 @@ print('output_images_dir :', output_images_dir)
 print('metadata_dir :', metadata_dir)
 print('metadata_images_dir :', metadata_images_dir)
 
-
 # ## II.3. FILES
 #Don't forget to put your data in the projname_data directory !
 # ### II.3.1. METADATA
@@ -137,6 +138,67 @@ 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
 
@@ -170,6 +232,68 @@ verify_line_no(filename, len(not_intensities))
 # Print to console
 print("not_intensities =\n", not_intensities)
 
+import os
+import pandas as pd
+
+# Function to compare headers (assuming you have this function defined in your my_modules.py)
+def compare_headers(expected, actual, description):
+    missing = [col for col in expected if col not in actual]
+    if missing:
+        print(f"WARNING: Missing expected columns in {description}: {missing}")
+    else:
+        print(f"All expected columns are present in {description}.")
+
+# 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'
+
+# Project and step names
+project_name = set_path               # Project name
+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)
+
+# Metadata directories
+metadata_dir = os.path.join(base_dir, project_name + "_metadata")
+metadata_images_dir = os.path.join(metadata_dir, "images")
+
+# Define writable directory
+writable_directory = '/tmp'
+
+# Check and read metadata file
+filename = "marker_intensity_metadata.csv"
+filename = os.path.join(metadata_dir, filename)
+
+# Check if the file exists
+if not os.path.exists(filename):
+    print("WARNING: Could not find desired file: " + filename)
+else:
+    print("The", filename, "file was imported for further analysis!")
+
+    # Open, read in information
+    metadata = pd.read_csv(filename)
+
+    # Verify headers
+    exp_cols = ['Round', 'Target', 'Channel', 'target_lower', 'full_column', 'marker', 'localisation']
+    compare_headers(exp_cols, metadata.columns.values, "Marker metadata file")
+
+    metadata = metadata.dropna()
+    print(metadata.head())
+
+    # Example of writing to the writable directory
+    output_file_path = os.path.join(writable_directory, 'processed_metadata.csv')
+    try:
+        metadata.to_csv(output_file_path, index=False)
+        print(f"Processed metadata 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.3.3. FULL_TO_SHORT_COLUMN_NAMES