added default value for base_path

dags/imageflow_dag.py

@@ -213,8 +213,8 @@ def imageflow_dag(**dag_input):
         
 
         # Create the base path directory if it doesn't exist
-        if not os.path.exists(f"{Variable.get('base_path')}"):
-            os.mkdir(f"{Variable.get('base_path')}")
+        if not os.path.exists(f"{Variable.get('base_output_path', 'placeholder')}"):
+            os.mkdir(f"{Variable.get('base_output_path', 'placeholder')}")
 
         # Load the scan configuration from the file
         with open("/scan_params/scan_config.json", "r") as conf:
@@ -227,8 +227,8 @@ def imageflow_dag(**dag_input):
         curr_conf_dict = prepare_current_scan_config(scan_config, tumor_activity_choice)
 
         # Save the current scan configuration to a file
-        with open(f"{Variable.get('base_path')}/curr_scan_config.json", "w+") as curr_conf:
-            print(f"Directory scan params written to: {Variable.get('base_path')}")
+        with open(f"{Variable.get('base_output_path', 'placeholder')}/curr_scan_config.json", "w+") as curr_conf:
+            print(f"Directory scan params written to: {Variable.get('base_output_path', 'placeholder')}")
             json.dump(curr_conf_dict, curr_conf)
 
         return 0
@@ -241,9 +241,9 @@ def imageflow_dag(**dag_input):
         
         # TODO: Copy all macros file data files
 
-        shutil.copytree('/gate_output/NCSA_RubInWater/Macros', f"{Variable.get('base_path')}/Macros")
-        shutil.copytree('/gate_output/NCSA_RubInWater/Data', f"{Variable.get('base_path')}/Data")
-        shutil.copy('/gate_output/NCSA_RubInWater/main.mac', f"{Variable.get('base_path')}/main.mac")
+        shutil.copytree('/gate_output/NCSA_RubInWater/Macros', f"{Variable.get('base_output_path', 'placeholder')}/Macros")
+        shutil.copytree('/gate_output/NCSA_RubInWater/Data', f"{Variable.get('base_output_path', 'placeholder')}/Data")
+        shutil.copy('/gate_output/NCSA_RubInWater/main.mac', f"{Variable.get('base_output_path', 'placeholder')}/main.mac")
 
         return 0
 
@@ -259,20 +259,20 @@ def imageflow_dag(**dag_input):
         # TODO: Replace the macros with user selected values
 
         # Open the current scan configuration file
-        with open(f"{Variable.get('base_path')}/curr_scan_config.json", "r+") as curr_conf:
+        with open(f"{Variable.get('base_output_path', 'placeholder')}/curr_scan_config.json", "r+") as curr_conf:
             curr_conf = json.load(curr_conf)
         
         # Set the activity file property for the GATE simulation software
         activity_file_property = "/gate/source/voxel_blob/imageReader/rangeTranslator/readTable"
         activity_file_value = curr_conf["activity_file"]
-        set_macro_property(f"{Variable.get('base_path')}/Macros/VoxelizedSource.mac", activity_file_property, activity_file_value, f"{Variable.get('base_path')}/Macros/VoxelizedSource.mac")
+        set_macro_property(f"{Variable.get('base_output_path', 'placeholder')}/Macros/VoxelizedSource.mac", activity_file_property, activity_file_value, f"{Variable.get('base_output_path', 'placeholder')}/Macros/VoxelizedSource.mac")
 
-        main_mac_file = f"{Variable.get('base_path')}/main.mac"
+        main_mac_file = f"{Variable.get('base_output_path', 'placeholder')}/main.mac"
 
         for component in range(20):
             # Set the output file property for the GATE simulation software
             
-            new_mac_file = f"{Variable.get('base_path')}/main_{component}.mac"
+            new_mac_file = f"{Variable.get('base_output_path', 'placeholder')}/main_{component}.mac"
 
             output_mac_file_property = "/control/execute"
             original_output_file_value = "Macros/Output.mac"
@@ -281,12 +281,12 @@ def imageflow_dag(**dag_input):
 
             output_file_property = "/gate/output/root/setFileName"
             output_file_value = f"Output/output_{component}.root"
-            set_macro_property(f"{Variable.get('base_path')}/Macros/Output.mac", output_file_property, output_file_value, f"{Variable.get('base_path')}/Macros/Output_{component}.mac")
+            set_macro_property(f"{Variable.get('base_output_path', 'placeholder')}/Macros/Output.mac", output_file_property, output_file_value, f"{Variable.get('base_output_path', 'placeholder')}/Macros/Output_{component}.mac")
 
         
         # Create the Output directory if it doesn't exist
-        if not os.path.exists(f"{Variable.get('base_path')}/Output"):
-            os.makedirs(f"{Variable.get('base_path')}/Output")
+        if not os.path.exists(f"{Variable.get('base_output_path', 'placeholder')}/Output"):
+            os.makedirs(f"{Variable.get('base_output_path', 'placeholder')}/Output")
 
         return 0
 
@@ -305,10 +305,10 @@ def imageflow_dag(**dag_input):
             print(f"Folder does not exist: {Variable.get('base_output_path', 'placeholder')}")
 
         # Move the output files from the pipeline to the output directory
-        shutil.copytree(Variable.get('base_path'), Variable.get('base_output_path', 'placeholder'))
+        shutil.copytree(Variable.get('base_output_path', 'placeholder'), Variable.get('base_output_path', 'placeholder'))
 
         # Remove the pipeline output directory  
-        shutil.rmtree(Variable.get('base_path'))
+        shutil.rmtree(Variable.get('base_output_path', 'placeholder'))
 
         # Copy the castor reconstruction script to the output directory
         shutil.copy("/castor_files/castor_reconstruction.sh", Variable.get('base_output_path', 'placeholder'))
@@ -338,7 +338,7 @@ def imageflow_dag(**dag_input):
         get_image_statistics: Get layer wise mean values for the volume
         """
         # Remove the output.root file from the base path
-        os.remove(f"{Variable.get('base_path')}/Output/output.root.root")
+        os.remove(f"{Variable.get('base_output_path', 'placeholder')}/Output/output.root.root")
 
 
         img_mean_stats = []
@@ -384,7 +384,7 @@ def imageflow_dag(**dag_input):
         img_mean_stats, img_sd_stats = get_image_statistics(stack_of_images)
 
         with open('/castor_files/stats_output/img_statistics.csv','a') as fd:
-            fd.write(f"{Variable.get('base_path')},{img_mean_stats},{img_sd_stats}\n")
+            fd.write(f"{Variable.get('base_output_path', 'placeholder')},{img_mean_stats},{img_sd_stats}\n")
             print("Statistics written to file")
 
             return 0
@@ -429,7 +429,7 @@ def imageflow_dag(**dag_input):
         volumes=[gate_volume, gate_output_volume, gate_scan_params_volume, gate_output_pipeline_volume],
         volume_mounts=[gate_volume_mount, gate_output_volume_mount, gate_scan_params_volume_mount, gate_output_pipeline_volume_mount],
         cmds=["/gate_files/gate_runner/runGate.sh"],
-        arguments=[Variable.get('base_path'), f"main_{i}.mac"], 
+        arguments=[Variable.get('base_output_path', 'placeholder'), f"main_{i}.mac"], 
         execution_timeout = timedelta(minutes=30),
         get_logs=True,
         affinity={