First commit for file handling

src/DataLib/fendl32B_retrofit/file_handling.py

@@ -0,0 +1,72 @@
+# Import packages
+from pathlib import Path
+
+def get_isotope(stem):
+    """
+    Extract the element name and mass number from a given filename.
+
+    Arguments:
+        stem (str): Stem of a an ENDF (TENDL) and/or PENDF file, formatted
+            as f'{element}{mass_number}.ext'
+    Returns:
+        element (str): Chemical symbol of the isotope whose data is contained
+            in the file.
+        A (str): Mass number of the isotope, potentially including the letter
+            "m" at the end if the isotope is in a metastable state.
+    """
+
+    isomer_id = ''
+
+    upper_case_letters = [char for char in stem if char.isupper()]
+    lower_case_letters = [char for char in stem if char.islower()]
+    numbers = [str(char) for char in stem if char.isdigit()]
+
+    if len(lower_case_letters) == 0:
+        lower_case_letters = ''
+    elif len(lower_case_letters) > 1:
+        isomer_id = lower_case_letters[-1]
+        lower_case_letters = lower_case_letters[:-1]
+
+    element = f'{upper_case_letters[0]}{lower_case_letters[0]}'
+    A = ''.join(numbers) + isomer_id
+
+    return element, A
+
+def search_for_files(directory = '.'):
+    """
+    Search through a directory for all pairs of ENDF (TENDL) and PENDF files
+        that have matching stems. If so, save the paths and the isotopic
+        information to a dictionary.
+    
+    Arguments:
+        directory (str, optional): Path to the directory in which to search
+            for ENDF and PENDF files.
+            Defaults to the present working directory (".").
+    Returns:
+        file_info (dict): Dictionary containing the chemical symbol, mass
+            number, and paths to the ENDF and PENDF files for a given isotope.
+            The dictionary is formatted as such:
+            {f'{element}{mass_number}' :
+                                        {'Element'} : Isotope's chemical symbol,
+                                        {'Mass Number'} : Isotope's mass number,
+                                        {'File Paths'} : (endf_path, pendf_path)
+            }
+    """
+
+    directory = Path(directory)
+
+    file_info = {}
+    for file in directory.iterdir():
+        if file.is_file():
+            if file.suffix == '.endf' or file.suffix == '.tendl':
+                endf_file = file
+                pendf_file = Path(f'{endf_file.stem}.pendf')
+                if pendf_file.is_file():
+                    element, A = get_isotope(file.stem)
+                    file_info[f'{element}{A}'] = {
+                        'Element'       :                 element,
+                        'Mass Number'   :                       A,
+                        'File Paths'    : (endf_file, pendf_file)
+                        }
+
+    return file_info

src/DataLib/fendl32B_retrofit/process_fendl3.2.py

@@ -2,30 +2,43 @@
 import reaction_data as rxd
 import tendl_processing as tp
 import groupr_tools
+import file_handling as fh
+from pandas import concat
 
 def main():
     """
     Main method when run as a command line script.
     """
 
+    TAPE20 = 'tape20'
+    TAPE21 = 'tape21'
+
     mt_dict = rxd.process_mt_data(rxd.load_mt_table('mt_table.csv'))
+    cumulative_data = tp.cumulative_data
 
-    endf_path = 'tape20'
-    pendf_path = 'tape21'
+    for isotope, file_properties in fh.search_for_files().items():
+        element = file_properties['Element']
+        A = file_properties['Mass Number']
+        endf_path, pendf_path = file_properties['File Paths']
+        endf_path.rename(TAPE20)
+        pendf_path.rename(TAPE21)
 
-    material_id, MTs, endftk_file_obj = tp.extract_endf_specs(endf_path)
-    njoy_input = groupr_tools.fill_input_template(material_id, MTs, 'Fe', 56, mt_dict)
-    groupr_tools.write_njoy_input_file(njoy_input)
-    gendf_path = groupr_tools.run_njoy('Fe', 56, material_id)
+        material_id, MTs, endftk_file_obj = tp.extract_endf_specs(TAPE20)
+        njoy_input = groupr_tools.fill_input_template(material_id, MTs,
+                                                      element, A, mt_dict)
+        groupr_tools.write_njoy_input_file(njoy_input)
+        gendf_path = groupr_tools.run_njoy(element, A, material_id)
 
-    pKZA = tp.extract_gendf_pkza(gendf_path)
-    # Extract MT values again from GENDF file as there may be some difference
-    # from the original MT values in the ENDF/PENDF files
-    material_id, MTs, endftk_file_obj = tp.extract_endf_specs(gendf_path)
-    gendf_data = tp.iterate_MTs(MTs, endftk_file_obj, mt_dict, pKZA)
-    gendf_data.to_csv('gendf_data.csv')
-    groupr_tools.cleanup_njoy_files()
+        pKZA = tp.extract_gendf_pkza(gendf_path)
+        # Extract MT values again from GENDF file as there may be some
+        # difference from the original MT values in the ENDF/PENDF files
+        material_id, MTs, endftk_file_obj = tp.extract_endf_specs(gendf_path)
+        gendf_data = tp.iterate_MTs(MTs, endftk_file_obj, mt_dict, pKZA)
+        cumulative_data = concat([cumulative_data, gendf_data],
+                                 ignore_index=True)
+        groupr_tools.cleanup_njoy_files()
 
+    cumulative_data.to_csv('cumulative_gendf_data.csv')
 
 if __name__ == '__main__':
     main()

src/DataLib/fendl32B_retrofit/tendl_processing.py

@@ -2,6 +2,15 @@
 import ENDFtk
 import pandas as pd
 
+# Initialize Data Frame in which to store all extracted data
+cumulative_data = pd.DataFrame({
+    'Parent KZA'            :       [],
+    'Daughter KZA'          :       [],
+    'Emitted Particles'     :       [],
+    'Non-Zero Groups'       :       [],
+    'Cross Sections'        :       []
+    })
+
 def extract_endf_specs(path):
     """
     Extract the material ID and MT numbers from an ENDF file.