Identify TENDL 2017 files for GROUPR processing and data extraction #68
Conversation
|
This looks like it needs a merge/rebase to resolve a conflict |
| 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 = upper_case_letters[0] + lower_case_letters[0] | ||
| A = ''.join(numbers) + isomer_id | ||
|
|
||
| return element, A |
There was a problem hiding this comment.
It seems like there must be a simpler way to do this? The files are always named n-Z[z]AAA[m], right, where
- Z is an uppercase letter
- [z] is an optional lower case letter
- A is a digit
- [m] is an optional ower case letter 'm'
so why not something like:
Z_start = 2
Z_end = Z_start + 1
if !stem[Z_end].isdigit():
Z_end += 1
element = stem[Z_start:Z_end]
A_start = Z_end
A_end = A_start + 3
if !stem[-1].isdigit():
A_end += 1
A = stem[A_start:A_end]
There was a problem hiding this comment.
regular expressions can make this even simpler in terms of number of lines, although maybe with a higher cognitive burden
| directory = Path(directory) | ||
|
|
||
| file_info = {} | ||
| for file in directory.iterdir(): |
There was a problem hiding this comment.
did you consider using directory.glob("*.endf")?
| endf_path.rename(TAPE20) | ||
| pendf_path.rename(TAPE21) |
There was a problem hiding this comment.
won't this result in gradually overwriting all the files in the directory? Don't we want to copy the files to these names for processing?
| endf_path.rename(TAPE20) | ||
| pendf_path.rename(TAPE21) |
There was a problem hiding this comment.
how did our prior testing work without a PENDF file? Do we really need a pendf file?
There was a problem hiding this comment.
We need an ENDF and a PENDF file to run GROUPR
| gendf_data = tp.iterate_MTs(MTs, endftk_file_obj, mt_dict, pKZA) | ||
| cumulative_data = concat([cumulative_data, gendf_data], | ||
| ignore_index=True) |
There was a problem hiding this comment.
Seeing how this is used across multiple nuclides, I'm not convinced that a pandas dataframe offers much more than a list of dictionaries. I think gendf_data could look like:
[ {'Parent KZA' : pkza, 'Daughger KZA' : dkza, etc.... } ,
{'Parent KZA' : pkza, 'Daughger KZA' : dkza, etc.... } , ... ]
and cumulative_data could be a local variable that gets appended with the new data. It will require a change to iterate_MTs() that I think will make that a little simpler too.
At the end, this list could be used to create a new dataframe and export to CVS:
pd.DataFrame(cumulative_data).to_csv(filename)
| for file in (p for p in dir.glob('*') if p.suffix in {'.tendl', '.endf'}): | ||
| if file.is_file() and file.with_suffix('.pendf').is_file(): | ||
| element, A = get_isotope(file.stem) | ||
| file_info[f'{element}{A}'] = { | ||
| 'Element' : element, | ||
| 'Mass Number' : A, | ||
| 'File Paths' : (file, file.with_suffix('.pendf')) | ||
| } |
There was a problem hiding this comment.
I was thinking that the glob could allow you to be more selective about which files you are even looking for:
| for file in (p for p in dir.glob('*') if p.suffix in {'.tendl', '.endf'}): | |
| if file.is_file() and file.with_suffix('.pendf').is_file(): | |
| element, A = get_isotope(file.stem) | |
| file_info[f'{element}{A}'] = { | |
| 'Element' : element, | |
| 'Mass Number' : A, | |
| 'File Paths' : (file, file.with_suffix('.pendf')) | |
| } | |
| for suffix in ['tendl', 'endf']: | |
| for file in dir.glob(f'*.{suffix}'): | |
| if file.with_suffix('.pendf').is_file(): | |
| element, A = get_isotope(file.stem) | |
| file_info[f'{element}{A}'] = { | |
| 'Element' : element, | |
| 'Mass Number' : A, | |
| 'File Paths' : (file, file.with_suffix('.pendf')) | |
| } |
| shutil.copy(endf_path, TAPE20) | ||
| shutil.copy(pendf_path, TAPE21) |
There was a problem hiding this comment.
I think this should work from Pathlib (trying to reduce number of dependencies, even if they're built in; I also think it's a more modern solution???):
| shutil.copy(endf_path, TAPE20) | |
| shutil.copy(pendf_path, TAPE21) | |
| Path(TAPE20).write_bytes(endf_path.read_bytes()) | |
| Path(TAPE21).write_bytes(pendf_path.read_bytes()) |
Closes #51 and #52.
Adds methods to search through a directory for pairs of ENDF and PENDF files corresponding to the same isotope to
tendl_processing.py.Modifies the example case in
process_fendl3.2.pyto be generalized to work with all of files found from the search methods employed in the new script.